data_IVC
#
_chem_comp.id IVC
_chem_comp.name "Isovaleryl-coenzyme A"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C26 H44 N7 O17 P3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbutanethioate"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-07-16
_chem_comp.pdbx_modified_date 2021-03-13
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 851.651
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code IVC
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 5CJV
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
IVC O9 O1 O 0 1 N N N N N N -206.289 -101.747 -35.376 -8.963 1.819 -0.384 O9 IVC 1
IVC P1 P1 P 0 1 N N N N N N -205.638 -103.094 -35.363 -9.332 0.283 -0.697 P1 IVC 2
IVC O5 O2 O 0 1 N N N N N N -205.352 -103.636 -36.766 -10.109 -0.277 0.432 O5 IVC 3
IVC O6 O3 O 0 1 N N N N N N -204.333 -103.113 -34.559 -10.212 0.206 -2.044 O6 IVC 4
IVC O2 O4 O 0 1 N N N N N N -206.602 -104.178 -34.668 -7.978 -0.565 -0.891 O2 IVC 5
IVC C1 C1 C 0 1 N N S N N N -208.043 -104.145 -34.582 -7.035 -0.778 0.162 C1 IVC 6
IVC C2 C2 C 0 1 N N R N N N -208.671 -104.286 -35.967 -6.771 -2.291 0.356 C2 IVC 7
IVC O3 O5 O 0 1 N N N N N N -207.835 -105.066 -36.814 -7.833 -3.069 -0.198 O3 IVC 8
IVC C4 C3 C 0 1 N N R N N N -209.958 -105.044 -35.627 -5.459 -2.496 -0.444 C4 IVC 9
IVC N1 N1 N 0 1 Y N N N N N -211.117 -104.196 -35.364 -4.728 -3.664 0.054 N1 IVC 10
IVC C7 C4 C 0 1 Y N N N N N -211.668 -103.917 -34.141 -3.723 -3.653 0.975 C7 IVC 11
IVC N2 N2 N 0 1 Y N N N N N -212.732 -103.153 -34.194 -3.300 -4.866 1.186 N2 IVC 12
IVC C8 C5 C 0 1 Y N N N N N -212.893 -102.909 -35.550 -4.005 -5.729 0.415 C8 IVC 13
IVC C6 C6 C 0 1 Y N N N N N -211.902 -103.542 -36.283 -4.933 -4.969 -0.316 C6 IVC 14
IVC N3 N3 N 0 1 Y N N N N N -211.754 -103.521 -37.612 -5.756 -5.588 -1.156 N3 IVC 15
IVC C15 C7 C 0 1 Y N N N N N -212.711 -102.788 -38.189 -5.704 -6.895 -1.305 C15 IVC 16
IVC N4 N4 N 0 1 Y N N N N N -213.722 -102.128 -37.617 -4.849 -7.650 -0.641 N4 IVC 17
IVC C12 C8 C 0 1 Y N N N N N -213.846 -102.168 -36.272 -3.991 -7.121 0.225 C12 IVC 18
IVC N5 N5 N 0 1 N N N N N N -214.861 -101.509 -35.705 -3.098 -7.921 0.916 N5 IVC 19
IVC O1 O6 O 0 1 N N N N N N -209.700 -105.817 -34.468 -4.716 -1.284 -0.191 O1 IVC 20
IVC C3 C9 C 0 1 N N R N N N -208.426 -105.450 -33.894 -5.659 -0.200 -0.222 C3 IVC 21
IVC C5 C10 C 0 1 N N N N N N -208.551 -105.368 -32.393 -5.248 0.876 0.785 C5 IVC 22
IVC O4 O7 O 0 1 N N N N N N -209.468 -104.308 -32.049 -4.028 1.487 0.358 O4 IVC 23
IVC P2 P2 P 0 1 N N N N N N -209.268 -103.417 -30.737 -3.302 2.665 1.181 P2 IVC 24
IVC O12 O8 O 0 1 N N N N N N -208.199 -103.909 -29.836 -4.242 3.972 1.189 O12 IVC 25
IVC O10 O9 O 0 1 N N N N N N -208.954 -101.988 -31.178 -3.064 2.220 2.572 O10 IVC 26
IVC O7 O10 O 0 1 N N N N N N -210.656 -103.390 -29.954 -1.896 3.020 0.482 O7 IVC 27
IVC P3 P3 P 0 1 N N N N N N -211.025 -103.649 -28.425 -0.554 3.756 0.981 P3 IVC 28
IVC O14 O11 O 0 1 N N N N N N -210.197 -104.753 -27.884 0.340 2.723 1.834 O14 IVC 29
IVC O13 O12 O 0 1 N N N N N N -212.499 -104.020 -28.355 -0.913 4.915 1.829 O13 IVC 30
IVC O8 O13 O 0 1 N N N N N N -210.835 -102.277 -27.637 0.285 4.264 -0.296 O8 IVC 31
IVC C11 C11 C 0 1 N N N N N N -209.865 -102.218 -26.582 1.476 5.047 -0.183 C11 IVC 32
IVC C9 C12 C 0 1 N N N N N N -209.500 -100.766 -26.280 2.017 5.356 -1.581 C9 IVC 33
IVC C13 C13 C 0 1 N N N N N N -208.685 -100.214 -27.455 2.334 4.047 -2.306 C13 IVC 34
IVC C14 C14 C 0 1 N N N N N N -210.795 -99.958 -26.142 0.966 6.137 -2.373 C14 IVC 35
IVC C10 C15 C 0 1 N N R N N N -208.672 -100.652 -24.975 3.291 6.194 -1.460 C10 IVC 36
IVC O11 O14 O 0 1 N N N N N N -208.400 -99.285 -24.725 2.971 7.470 -0.902 O11 IVC 37
IVC C16 C16 C 0 1 N N N N N N -209.390 -101.261 -23.782 4.275 5.487 -0.564 C16 IVC 38
IVC O15 O15 O 0 1 N N N N N N -209.356 -102.473 -23.588 4.515 5.927 0.540 O15 IVC 39
IVC N6 N6 N 0 1 N N N N N N -210.026 -100.414 -22.976 4.888 4.365 -0.990 N6 IVC 40
IVC C17 C17 C 0 1 N N N N N N -210.703 -100.844 -21.764 5.763 3.619 -0.083 C17 IVC 41
IVC C18 C18 C 0 1 N N N N N N -210.209 -100.088 -20.552 6.328 2.396 -0.809 C18 IVC 42
IVC C19 C19 C 0 1 N N N N N N -211.093 -100.308 -19.354 7.228 1.629 0.125 C19 IVC 43
IVC O16 O16 O 0 1 N N N N N N -212.193 -100.844 -19.460 7.402 2.022 1.259 O16 IVC 44
IVC N7 N7 N 0 1 N N N N N N -210.612 -99.890 -18.188 7.841 0.507 -0.301 N7 IVC 45
IVC C20 C20 C 0 1 N N N N N N -211.361 -100.023 -16.949 8.717 -0.239 0.606 C20 IVC 46
IVC C21 C21 C 0 1 N N N N N N -211.070 -98.900 -15.976 9.282 -1.461 -0.120 C21 IVC 47
IVC S1 S1 S 0 1 N N N N N N -212.350 -98.866 -14.693 10.363 -2.383 1.001 S1 IVC 48
IVC C22 C22 C 0 1 N N N N N N -211.746 -97.611 -13.618 10.845 -3.660 -0.033 C22 IVC 49
IVC O17 O17 O 0 1 N N N N N N -210.722 -97.016 -13.813 10.430 -3.707 -1.172 O17 IVC 50
IVC C23 C23 C 0 1 N N N N N N -212.645 -97.358 -12.437 11.784 -4.725 0.472 C23 IVC 51
IVC C24 C24 C 0 1 N N N N N N -211.899 -97.269 -11.110 12.051 -5.739 -0.642 C24 IVC 52
IVC C25 C25 C 0 1 N N N N N N -210.805 -98.311 -10.986 13.100 -6.749 -0.171 C25 IVC 53
IVC C26 C26 C 0 1 N N N N N N -211.284 -95.895 -10.976 10.753 -6.473 -0.985 C26 IVC 54
IVC H1 H1 H 0 1 N N N N N N -206.411 -101.463 -36.274 -8.453 2.251 -1.083 H1 IVC 55
IVC H2 H2 H 0 1 N N N N N N -203.632 -103.455 -35.101 -11.044 0.696 -1.999 H2 IVC 56
IVC H3 H3 H 0 1 N N N N N N -208.427 -103.266 -34.043 -7.392 -0.329 1.089 H3 IVC 57
IVC H4 H4 H 0 1 N N N N N N -208.900 -103.299 -36.396 -6.625 -2.528 1.410 H4 IVC 58
IVC H5 H5 H 0 1 N N N N N N -206.974 -104.668 -36.864 -7.673 -4.022 -0.182 H5 IVC 59
IVC H6 H6 H 0 1 N N N N N N -210.190 -105.712 -36.469 -5.672 -2.603 -1.508 H6 IVC 60
IVC H7 H7 H 0 1 N N N N N N -211.261 -104.294 -33.214 -3.336 -2.769 1.459 H7 IVC 61
IVC H8 H8 H 0 1 N N N N N N -212.660 -102.720 -39.266 -6.385 -7.366 -1.999 H8 IVC 62
IVC H9 H9 H 0 1 N N N N N N -215.405 -101.060 -36.414 -3.094 -8.880 0.772 H9 IVC 63
IVC H10 H10 H 0 1 N N N N N N -215.436 -102.153 -35.201 -2.477 -7.523 1.545 H10 IVC 64
IVC H11 H11 H 0 1 N N N N N N -207.674 -106.212 -34.145 -5.702 0.225 -1.225 H11 IVC 65
IVC H12 H12 H 0 1 N N N N N N -208.931 -106.324 -32.003 -6.030 1.633 0.848 H12 IVC 66
IVC H13 H13 H 0 1 N N N N N N -207.565 -105.158 -31.953 -5.102 0.421 1.765 H13 IVC 67
IVC H14 H14 H 0 1 N N N N N N -207.543 -103.231 -29.722 -4.440 4.319 0.308 H14 IVC 68
IVC H15 H15 H 0 1 N N N N N N -210.761 -105.465 -27.605 0.612 1.938 1.340 H15 IVC 69
IVC H16 H16 H 0 1 N N N N N N -210.284 -102.683 -25.677 1.250 5.980 0.333 H16 IVC 70
IVC H17 H17 H 0 1 N N N N N N -208.961 -102.763 -26.889 2.224 4.491 0.381 H17 IVC 71
IVC H18 H18 H 0 1 N N N N N N -208.413 -99.167 -27.254 1.411 3.493 -2.476 H18 IVC 72
IVC H19 H19 H 0 1 N N N N N N -207.771 -100.813 -27.580 2.806 4.267 -3.263 H19 IVC 73
IVC H20 H20 H 0 1 N N N N N N -209.286 -100.266 -28.375 3.010 3.448 -1.696 H20 IVC 74
IVC H21 H21 H 0 1 N N N N N N -211.384 -100.350 -25.300 0.652 7.009 -1.799 H21 IVC 75
IVC H22 H22 H 0 1 N N N N N N -210.550 -98.902 -25.958 1.393 6.461 -3.322 H22 IVC 76
IVC H23 H23 H 0 1 N N N N N N -211.380 -100.042 -27.070 0.104 5.497 -2.562 H23 IVC 77
IVC H24 H24 H 0 1 N N N N N N -207.728 -101.196 -25.124 3.731 6.330 -2.448 H24 IVC 78
IVC H25 H25 H 0 1 N N N N N N -207.892 -99.204 -23.926 2.574 7.426 -0.022 H25 IVC 79
IVC H26 H26 H 0 1 N N N N N N -210.039 -99.443 -23.214 4.749 4.051 -1.897 H26 IVC 80
IVC H27 H27 H 0 1 N N N N N N -211.783 -100.670 -21.878 6.583 4.260 0.240 H27 IVC 81
IVC H28 H28 H 0 1 N N N N N N -210.519 -101.918 -21.614 5.193 3.293 0.787 H28 IVC 82
IVC H29 H29 H 0 1 N N N N N N -209.192 -100.429 -20.311 5.508 1.755 -1.132 H29 IVC 83
IVC H30 H30 H 0 1 N N N N N N -210.189 -99.014 -20.787 6.899 2.722 -1.679 H30 IVC 84
IVC H31 H31 H 0 1 N N N N N N -209.705 -99.470 -18.162 7.703 0.193 -1.209 H31 IVC 85
IVC H32 H32 H 0 1 N N N N N N -212.436 -100.018 -17.183 9.537 0.403 0.929 H32 IVC 86
IVC H33 H33 H 0 1 N N N N N N -211.094 -100.979 -16.475 8.146 -0.564 1.476 H33 IVC 87
IVC H34 H34 H 0 1 N N N N N N -210.087 -99.064 -15.510 8.462 -2.103 -0.443 H34 IVC 88
IVC H35 H35 H 0 1 N N N N N N -211.065 -97.941 -16.514 9.852 -1.136 -0.990 H35 IVC 89
IVC H36 H36 H 0 1 N N N N N N -213.176 -96.409 -12.601 12.724 -4.265 0.778 H36 IVC 90
IVC H37 H37 H 0 1 N N N N N N -213.373 -98.180 -12.372 11.333 -5.232 1.325 H37 IVC 91
IVC H38 H38 H 0 1 N N N N N N -212.620 -97.415 -10.292 12.419 -5.219 -1.526 H38 IVC 92
IVC H39 H39 H 0 1 N N N N N N -210.302 -98.201 -10.014 12.732 -7.269 0.713 H39 IVC 93
IVC H40 H40 H 0 1 N N N N N N -211.246 -99.316 -11.059 13.290 -7.471 -0.965 H40 IVC 94
IVC H41 H41 H 0 1 N N N N N N -210.073 -98.172 -11.795 14.024 -6.226 0.073 H41 IVC 95
IVC H42 H42 H 0 1 N N N N N N -210.745 -95.826 -10.020 10.386 -6.993 -0.101 H42 IVC 96
IVC H43 H43 H 0 1 N N N N N N -210.582 -95.725 -11.806 10.007 -5.753 -1.320 H43 IVC 97
IVC H44 H44 H 0 1 N N N N N N -212.078 -95.134 -11.005 10.944 -7.195 -1.779 H44 IVC 98
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
IVC C15 N4 DOUB Y N 1
IVC C15 N3 SING Y N 2
IVC N4 C12 SING Y N 3
IVC N3 C6 DOUB Y N 4
IVC O3 C2 SING N N 5
IVC O5 P1 DOUB N N 6
IVC C6 C8 SING Y N 7
IVC C6 N1 SING Y N 8
IVC C12 N5 SING N N 9
IVC C12 C8 DOUB Y N 10
IVC C2 C4 SING N N 11
IVC C2 C1 SING N N 12
IVC C4 N1 SING N N 13
IVC C4 O1 SING N N 14
IVC C8 N2 SING Y N 15
IVC O9 P1 SING N N 16
IVC N1 C7 SING Y N 17
IVC P1 O2 SING N N 18
IVC P1 O6 SING N N 19
IVC O2 C1 SING N N 20
IVC C1 C3 SING N N 21
IVC O1 C3 SING N N 22
IVC N2 C7 DOUB Y N 23
IVC C3 C5 SING N N 24
IVC C5 O4 SING N N 25
IVC O4 P2 SING N N 26
IVC O10 P2 DOUB N N 27
IVC P2 O7 SING N N 28
IVC P2 O12 SING N N 29
IVC O7 P3 SING N N 30
IVC P3 O13 DOUB N N 31
IVC P3 O14 SING N N 32
IVC P3 O8 SING N N 33
IVC O8 C11 SING N N 34
IVC C13 C9 SING N N 35
IVC C11 C9 SING N N 36
IVC C9 C14 SING N N 37
IVC C9 C10 SING N N 38
IVC C10 O11 SING N N 39
IVC C10 C16 SING N N 40
IVC C16 O15 DOUB N N 41
IVC C16 N6 SING N N 42
IVC N6 C17 SING N N 43
IVC C17 C18 SING N N 44
IVC C18 C19 SING N N 45
IVC O16 C19 DOUB N N 46
IVC C19 N7 SING N N 47
IVC N7 C20 SING N N 48
IVC C20 C21 SING N N 49
IVC C21 S1 SING N N 50
IVC S1 C22 SING N N 51
IVC O17 C22 DOUB N N 52
IVC C22 C23 SING N N 53
IVC C23 C24 SING N N 54
IVC C24 C25 SING N N 55
IVC C24 C26 SING N N 56
IVC O9 H1 SING N N 57
IVC O6 H2 SING N N 58
IVC C1 H3 SING N N 59
IVC C2 H4 SING N N 60
IVC O3 H5 SING N N 61
IVC C4 H6 SING N N 62
IVC C7 H7 SING N N 63
IVC C15 H8 SING N N 64
IVC N5 H9 SING N N 65
IVC N5 H10 SING N N 66
IVC C3 H11 SING N N 67
IVC C5 H12 SING N N 68
IVC C5 H13 SING N N 69
IVC O12 H14 SING N N 70
IVC O14 H15 SING N N 71
IVC C11 H16 SING N N 72
IVC C11 H17 SING N N 73
IVC C13 H18 SING N N 74
IVC C13 H19 SING N N 75
IVC C13 H20 SING N N 76
IVC C14 H21 SING N N 77
IVC C14 H22 SING N N 78
IVC C14 H23 SING N N 79
IVC C10 H24 SING N N 80
IVC O11 H25 SING N N 81
IVC N6 H26 SING N N 82
IVC C17 H27 SING N N 83
IVC C17 H28 SING N N 84
IVC C18 H29 SING N N 85
IVC C18 H30 SING N N 86
IVC N7 H31 SING N N 87
IVC C20 H32 SING N N 88
IVC C20 H33 SING N N 89
IVC C21 H34 SING N N 90
IVC C21 H35 SING N N 91
IVC C23 H36 SING N N 92
IVC C23 H37 SING N N 93
IVC C24 H38 SING N N 94
IVC C25 H39 SING N N 95
IVC C25 H40 SING N N 96
IVC C25 H41 SING N N 97
IVC C26 H42 SING N N 98
IVC C26 H43 SING N N 99
IVC C26 H44 SING N N 100
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
IVC SMILES ACDLabs 12.01 OP(OC1C(OC(C1O)n2cnc3c2ncnc3N)COP(OP(=O)(O)OCC(C)(C(O)C(=O)NCCC(NCCSC(CC(C)C)=O)=O)C)(O)=O)(O)=O
IVC InChI InChI 1.03 InChI=1S/C26H44N7O17P3S/c1-14(2)9-17(35)54-8-7-28-16(34)5-6-29-24(38)21(37)26(3,4)11-47-53(44,45)50-52(42,43)46-10-15-20(49-51(39,40)41)19(36)25(48-15)33-13-32-18-22(27)30-12-31-23(18)33/h12-15,19-21,25,36-37H,5-11H2,1-4H3,(H,28,34)(H,29,38)(H,42,43)(H,44,45)(H2,27,30,31)(H2,39,40,41)/t15-,19-,20-,21+,25-/m1/s1
IVC InChIKey InChI 1.03 UYVZIWWBJMYRCD-ZMHDXICWSA-N
IVC SMILES_CANONICAL CACTVS 3.385 CC(C)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
IVC SMILES CACTVS 3.385 CC(C)CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
IVC SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 CC(C)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
IVC SMILES "OpenEye OEToolkits" 1.9.2 CC(C)CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
IVC "SYSTEMATIC NAME" ACDLabs 12.01 "S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 3-methylbutanethioate (non-preferred name)"
IVC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbutanethioate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
IVC 'Create component' 2015-07-16 RCSB
IVC 'Initial release' 2015-09-09 RCSB
IVC 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id IVC
_pdbx_chem_comp_synonyms.name
"S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbutanethioate"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id IVC
_pdbe_chem_comp_synonyms.name
'S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbutanethioate'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
IVC O9 O 28.728 -3.258 1
IVC P1 P 27.236 -3.412 2
IVC O5 O 27.082 -1.920 3
IVC O6 O 25.744 -3.566 4
IVC O2 O 27.390 -4.904 5
IVC C1 C 26.175 -5.783 6
IVC C2 C 26.173 -7.283 7
IVC O3 O 27.385 -8.167 8
IVC C4 C 24.745 -7.745 9
IVC N1 N 24.279 -9.170 10
IVC C7 C 25.155 -10.377 11
IVC N2 N 24.279 -11.584 12
IVC C8 C 22.860 -11.127 13
IVC C6 C 22.860 -9.627 14
IVC N3 N 21.561 -8.877 15
IVC C15 C 20.262 -9.627 16
IVC N4 N 20.262 -11.127 17
IVC C12 C 21.561 -11.877 18
IVC N5 N 21.561 -13.377 19
IVC O1 O 23.866 -6.529 20
IVC C3 C 24.750 -5.317 21
IVC C5 C 24.289 -3.890 22
IVC O4 O 22.822 -3.576 23
IVC P2 P 22.361 -2.148 24
IVC O12 O 23.788 -1.687 25
IVC O10 O 20.934 -2.609 26
IVC O7 O 21.900 -0.721 27
IVC P3 P 20.433 -0.406 28
IVC O14 O 20.119 -1.873 29
IVC O13 O 20.748 1.060 30
IVC O8 O 18.966 -0.092 31
IVC C11 C 18.505 1.335 32
IVC C9 C 17.039 1.650 33
IVC C13 C 17.353 3.116 34
IVC C14 C 16.724 0.183 35
IVC C10 C 15.572 1.964 36
IVC O11 O 14.566 0.851 37
IVC C16 C 15.111 3.392 38
IVC O15 O 16.117 4.505 39
IVC N6 N 13.644 3.706 40
IVC C17 C 13.183 5.133 41
IVC C18 C 11.716 5.448 42
IVC C19 C 11.255 6.875 43
IVC O16 O 12.261 7.988 44
IVC N7 N 9.789 7.189 45
IVC C20 C 9.328 8.617 46
IVC C21 C 7.861 8.931 47
IVC S1 S 7.400 10.359 48
IVC C22 C 5.933 10.673 49
IVC O17 O 4.928 9.560 50
IVC C23 C 5.472 12.101 51
IVC C24 C 4.006 12.415 52
IVC C25 C 3.545 13.842 53
IVC C26 C 3.000 11.302 54
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
IVC C15 N4 DOUBLE NONE 1
IVC C15 N3 SINGLE NONE 2
IVC N4 C12 SINGLE NONE 3
IVC N3 C6 DOUBLE NONE 4
IVC C2 O3 SINGLE BEGINWEDGE 5
IVC O5 P1 DOUBLE NONE 6
IVC C6 C8 SINGLE NONE 7
IVC C6 N1 SINGLE NONE 8
IVC C12 N5 SINGLE NONE 9
IVC C12 C8 DOUBLE NONE 10
IVC C2 C4 SINGLE NONE 11
IVC C2 C1 SINGLE NONE 12
IVC C4 N1 SINGLE BEGINDASH 13
IVC C4 O1 SINGLE NONE 14
IVC C8 N2 SINGLE NONE 15
IVC O9 P1 SINGLE NONE 16
IVC N1 C7 SINGLE NONE 17
IVC P1 O2 SINGLE NONE 18
IVC P1 O6 SINGLE NONE 19
IVC C1 O2 SINGLE BEGINWEDGE 20
IVC C1 C3 SINGLE NONE 21
IVC O1 C3 SINGLE NONE 22
IVC N2 C7 DOUBLE NONE 23
IVC C3 C5 SINGLE BEGINDASH 24
IVC C5 O4 SINGLE NONE 25
IVC O4 P2 SINGLE NONE 26
IVC O10 P2 DOUBLE NONE 27
IVC P2 O7 SINGLE NONE 28
IVC P2 O12 SINGLE BEGINDASH 29
IVC O7 P3 SINGLE NONE 30
IVC P3 O13 DOUBLE NONE 31
IVC P3 O14 SINGLE BEGINDASH 32
IVC P3 O8 SINGLE NONE 33
IVC O8 C11 SINGLE NONE 34
IVC C13 C9 SINGLE NONE 35
IVC C11 C9 SINGLE NONE 36
IVC C9 C14 SINGLE NONE 37
IVC C9 C10 SINGLE NONE 38
IVC C10 O11 SINGLE BEGINWEDGE 39
IVC C10 C16 SINGLE NONE 40
IVC C16 O15 DOUBLE NONE 41
IVC C16 N6 SINGLE NONE 42
IVC N6 C17 SINGLE NONE 43
IVC C17 C18 SINGLE NONE 44
IVC C18 C19 SINGLE NONE 45
IVC O16 C19 DOUBLE NONE 46
IVC C19 N7 SINGLE NONE 47
IVC N7 C20 SINGLE NONE 48
IVC C20 C21 SINGLE NONE 49
IVC C21 S1 SINGLE NONE 50
IVC S1 C22 SINGLE NONE 51
IVC O17 C22 DOUBLE NONE 52
IVC C22 C23 SINGLE NONE 53
IVC C23 C24 SINGLE NONE 54
IVC C24 C25 SINGLE NONE 55
IVC C24 C26 SINGLE NONE 56
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
IVC MurckoScaffold S1 scaffold 'c1ncc2ncn([C@H]3CCCO3)c2n1' InChI=1S/C9H10N4O/c1-2-8(14-3-1)13-6-12-7-4-10-5-11-9(7)13/h4-6,8H,1-3H2/t8-/m1/s1 DAKONNSVCLKUJN-MRVPVSSYSA-N
IVC adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
IVC amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
IVC imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
IVC phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
IVC purine F5 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
IVC pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
IVC ribose F7 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
IVC C1 S1 1
IVC C2 S1 1
IVC C4 S1 1
IVC N1 S1 1
IVC C7 S1 1
IVC N2 S1 1
IVC C8 S1 1
IVC C6 S1 1
IVC N3 S1 1
IVC C15 S1 1
IVC N4 S1 1
IVC C12 S1 1
IVC O1 S1 1
IVC C3 S1 1
IVC N4 F1 1
IVC C12 F1 1
IVC C8 F1 1
IVC C6 F1 1
IVC N3 F1 1
IVC C15 F1 1
IVC N1 F1 1
IVC C7 F1 1
IVC N2 F1 1
IVC N5 F1 1
IVC N6 F2 1
IVC C16 F2 1
IVC O15 F2 1
IVC C10 F2 1
IVC N7 F2 2
IVC C19 F2 2
IVC O16 F2 2
IVC C18 F2 2
IVC C8 F3 1
IVC C6 F3 1
IVC N1 F3 1
IVC C7 F3 1
IVC N2 F3 1
IVC O9 F4 1
IVC P1 F4 1
IVC O5 F4 1
IVC O2 F4 1
IVC O6 F4 1
IVC O4 F4 2
IVC P2 F4 2
IVC O10 F4 2
IVC O7 F4 2
IVC O12 F4 2
IVC O7 F4 3
IVC P3 F4 3
IVC O13 F4 3
IVC O14 F4 3
IVC O8 F4 3
IVC N2 F5 1
IVC C7 F5 1
IVC N1 F5 1
IVC C6 F5 1
IVC C8 F5 1
IVC C12 F5 1
IVC N4 F5 1
IVC C15 F5 1
IVC N3 F5 1
IVC C8 F6 1
IVC C6 F6 1
IVC N3 F6 1
IVC C15 F6 1
IVC N4 F6 1
IVC C12 F6 1
IVC C2 F7 1
IVC C1 F7 1
IVC C3 F7 1
IVC O1 F7 1
IVC C4 F7 1
IVC C5 F7 1
IVC O4 F7 1
IVC O2 F7 1
IVC O3 F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id IVC
_pdbe_chem_comp_rdkit_properties.exactmw 851.173
_pdbe_chem_comp_rdkit_properties.amw 851.659
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 24
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 32
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 23
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 54
_pdbe_chem_comp_rdkit_properties.NumAtoms 98
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 28
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.692
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 7
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 374.449
_pdbe_chem_comp_rdkit_properties.tpsa 363.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.098
_pdbe_chem_comp_rdkit_properties.CrippenMR 183.523
_pdbe_chem_comp_rdkit_properties.chi0v 28.320
_pdbe_chem_comp_rdkit_properties.chi1v 17.469
_pdbe_chem_comp_rdkit_properties.chi2v 7.727
_pdbe_chem_comp_rdkit_properties.chi3v 7.727
_pdbe_chem_comp_rdkit_properties.chi4v 5.145
_pdbe_chem_comp_rdkit_properties.chi0n 68.821
_pdbe_chem_comp_rdkit_properties.chi1n 33.509
_pdbe_chem_comp_rdkit_properties.chi2n 4.610
_pdbe_chem_comp_rdkit_properties.chi3n 4.610
_pdbe_chem_comp_rdkit_properties.chi4n 2.729
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.440
_pdbe_chem_comp_rdkit_properties.kappa1 13.848
_pdbe_chem_comp_rdkit_properties.kappa2 19.135
_pdbe_chem_comp_rdkit_properties.kappa3 13.940
_pdbe_chem_comp_rdkit_properties.Phi 4.907
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
IVC UniChem ChEBI 15487
IVC UniChem ZINC ZINC000008551494
IVC UniChem SureChEMBL SCHEMBL850285
IVC UniChem HMDB HMDB0001113
IVC UniChem NMRShiftDB 60020431
IVC UniChem Nikkaji J675.058C
IVC UniChem LipidMaps LMFA07050336
IVC UniChem MetaboLights MTBLC15487
IVC UniChem BRENDA 116685
IVC UniChem BRENDA 12351
IVC UniChem BRENDA 784
IVC UniChem BRENDA 91507
IVC UniChem BRENDA 91514
IVC UniChem BRENDA 9187
IVC UniChem PubChem 165435
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
IVC O9 -3.472 -4.216 2.628 ETKDGv3 1
IVC P1 -3.209 -4.403 0.966 ETKDGv3 2
IVC O5 -3.949 -5.628 0.481 ETKDGv3 3
IVC O6 -1.553 -4.601 0.674 ETKDGv3 4
IVC O2 -3.782 -3.035 0.122 ETKDGv3 5
IVC C1 -3.226 -1.861 0.688 ETKDGv3 6
IVC C2 -3.020 -0.827 -0.386 ETKDGv3 7
IVC O3 -2.672 -1.422 -1.611 ETKDGv3 8
IVC C4 -4.380 -0.144 -0.455 ETKDGv3 9
IVC N1 -4.240 1.274 -0.788 ETKDGv3 10
IVC C7 -3.883 2.344 0.115 ETKDGv3 11
IVC N2 -3.408 3.419 -0.458 ETKDGv3 12
IVC C8 -3.397 3.125 -1.848 ETKDGv3 13
IVC C6 -3.891 1.814 -2.047 ETKDGv3 14
IVC N3 -3.871 1.217 -3.199 ETKDGv3 15
IVC C15 -3.370 1.967 -4.331 ETKDGv3 16
IVC N4 -2.914 3.189 -4.171 ETKDGv3 17
IVC C12 -2.900 3.820 -2.870 ETKDGv3 18
IVC N5 -2.344 5.124 -2.697 ETKDGv3 19
IVC O1 -5.027 -0.286 0.794 ETKDGv3 20
IVC C3 -4.265 -1.178 1.582 ETKDGv3 21
IVC C5 -3.611 -0.397 2.732 ETKDGv3 22
IVC O4 -2.871 -1.274 3.549 ETKDGv3 23
IVC P2 -2.112 -0.362 4.776 ETKDGv3 24
IVC O12 -3.257 0.003 5.967 ETKDGv3 25
IVC O10 -1.027 -1.217 5.397 ETKDGv3 26
IVC O7 -1.521 1.111 4.132 ETKDGv3 27
IVC P3 0.170 1.183 4.321 ETKDGv3 28
IVC O14 0.568 1.072 5.963 ETKDGv3 29
IVC O13 0.655 2.517 3.800 ETKDGv3 30
IVC O8 0.961 -0.063 3.462 ETKDGv3 31
IVC C11 0.399 -0.167 2.171 ETKDGv3 32
IVC C9 1.344 -0.966 1.234 ETKDGv3 33
IVC C13 0.623 -1.186 -0.116 ETKDGv3 34
IVC C14 2.614 -0.119 0.992 ETKDGv3 35
IVC C10 1.721 -2.340 1.883 ETKDGv3 36
IVC O11 0.553 -3.035 2.246 ETKDGv3 37
IVC C16 2.563 -3.205 0.970 ETKDGv3 38
IVC O15 1.999 -4.016 0.185 ETKDGv3 39
IVC N6 3.993 -3.080 0.974 ETKDGv3 40
IVC C17 4.868 -3.844 0.085 ETKDGv3 41
IVC C18 5.641 -2.910 -0.853 ETKDGv3 42
IVC C19 4.756 -2.273 -1.889 ETKDGv3 43
IVC O16 4.076 -3.006 -2.658 ETKDGv3 44
IVC N7 4.741 -0.846 -2.051 ETKDGv3 45
IVC C20 4.100 -0.184 -3.187 ETKDGv3 46
IVC C21 2.582 -0.188 -3.035 ETKDGv3 47
IVC S1 1.812 0.768 -4.390 ETKDGv3 48
IVC C22 0.748 1.773 -3.342 ETKDGv3 49
IVC O17 -0.242 1.267 -2.838 ETKDGv3 50
IVC C23 0.989 3.256 -3.212 ETKDGv3 51
IVC C24 1.444 3.733 -1.812 ETKDGv3 52
IVC C25 0.500 3.284 -0.688 ETKDGv3 53
IVC C26 2.893 3.337 -1.507 ETKDGv3 54
IVC H1 -2.969 -4.959 3.049 ETKDGv3 55
IVC H2 -1.450 -4.460 -0.301 ETKDGv3 56
IVC H3 -2.255 -2.034 1.207 ETKDGv3 57
IVC H4 -2.233 -0.107 -0.054 ETKDGv3 58
IVC H5 -2.206 -0.726 -2.142 ETKDGv3 59
IVC H6 -5.012 -0.636 -1.227 ETKDGv3 60
IVC H7 -3.990 2.268 1.188 ETKDGv3 61
IVC H8 -3.362 1.516 -5.313 ETKDGv3 62
IVC H9 -2.314 5.580 -1.758 ETKDGv3 63
IVC H10 -1.950 5.635 -3.518 ETKDGv3 64
IVC H11 -4.949 -1.937 2.023 ETKDGv3 65
IVC H12 -4.415 0.097 3.324 ETKDGv3 66
IVC H13 -2.953 0.379 2.284 ETKDGv3 67
IVC H14 -3.672 -0.868 6.194 ETKDGv3 68
IVC H15 1.556 1.008 5.979 ETKDGv3 69
IVC H16 -0.574 -0.692 2.241 ETKDGv3 70
IVC H17 0.210 0.834 1.714 ETKDGv3 71
IVC H18 0.268 -0.223 -0.537 ETKDGv3 72
IVC H19 1.300 -1.655 -0.858 ETKDGv3 73
IVC H20 -0.250 -1.857 0.008 ETKDGv3 74
IVC H21 2.349 0.889 0.609 ETKDGv3 75
IVC H22 3.275 -0.597 0.243 ETKDGv3 76
IVC H23 3.188 0.010 1.934 ETKDGv3 77
IVC H24 2.315 -2.140 2.805 ETKDGv3 78
IVC H25 0.822 -3.735 2.897 ETKDGv3 79
IVC H26 4.439 -2.412 1.643 ETKDGv3 80
IVC H27 4.299 -4.594 -0.505 ETKDGv3 81
IVC H28 5.598 -4.405 0.708 ETKDGv3 82
IVC H29 6.423 -3.498 -1.379 ETKDGv3 83
IVC H30 6.160 -2.132 -0.252 ETKDGv3 84
IVC H31 5.302 -0.257 -1.395 ETKDGv3 85
IVC H32 4.453 0.870 -3.236 ETKDGv3 86
IVC H33 4.394 -0.689 -4.133 ETKDGv3 87
IVC H34 2.200 -1.228 -3.096 ETKDGv3 88
IVC H35 2.309 0.218 -2.043 ETKDGv3 89
IVC H36 0.050 3.783 -3.484 ETKDGv3 90
IVC H37 1.746 3.570 -3.963 ETKDGv3 91
IVC H38 1.415 4.845 -1.832 ETKDGv3 92
IVC H39 0.781 3.782 0.265 ETKDGv3 93
IVC H40 0.555 2.188 -0.534 ETKDGv3 94
IVC H41 -0.545 3.565 -0.929 ETKDGv3 95
IVC H42 2.994 2.243 -1.391 ETKDGv3 96
IVC H43 3.567 3.675 -2.322 ETKDGv3 97
IVC H44 3.226 3.818 -0.562 ETKDGv3 98
#