data_YAS
#
_chem_comp.id YAS
_chem_comp.name
"~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{R},4~{S},5~{R})-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] butanethioate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H42 N7 O17 P3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms Butyryl-CoA
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-12-06
_chem_comp.pdbx_modified_date 2021-03-01
_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 837.624
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YAS
_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 6NA4
_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
YAS C1B C1 C 0 1 N N R N N N -17.529 8.515 -4.241 -7.172 0.303 -0.846 C1B YAS 1
YAS C2A C2 C 0 1 Y N N N N N -15.473 11.540 -6.443 -9.306 -1.740 -4.225 C2A YAS 2
YAS C2B C3 C 0 1 N N S N N N -18.785 8.840 -4.070 -8.027 -0.272 0.305 C2B YAS 3
YAS C2P C4 C 0 1 N N N N N N -16.078 -10.760 -7.033 10.271 -1.955 -0.248 C2P YAS 4
YAS C3B C5 C 0 1 N N R N N N -19.123 8.077 -2.809 -7.003 -0.553 1.428 C3B YAS 5
YAS C3P C6 C 0 1 N N N N N N -16.868 -10.342 -5.787 9.702 -0.647 0.307 C3P YAS 6
YAS C4A C7 C 0 1 Y N N N N N -16.358 9.439 -6.135 -7.581 -1.281 -2.777 C4A YAS 7
YAS C4B C8 C 0 1 N N S N N N -18.437 6.741 -3.229 -5.652 -0.115 0.822 C4B YAS 8
YAS C5A C9 C 0 1 Y N N N N N -15.930 9.034 -7.386 -6.803 -2.266 -3.409 C5A YAS 9
YAS C5B C10 C 0 1 N N N N N N -18.435 5.576 -2.202 -4.777 0.542 1.893 C5B YAS 10
YAS C5P C11 C 0 1 N N N N N N -16.039 -7.994 -5.341 7.996 0.986 -0.291 C5P YAS 11
YAS C6A C12 C 0 1 Y N N N N N -15.243 9.986 -8.163 -7.368 -2.965 -4.490 C6A YAS 12
YAS C6P C13 C 0 1 N N N N N N -16.317 -6.490 -5.318 6.909 1.489 -1.206 C6P YAS 13
YAS C7P C14 C 0 1 N N N N N N -17.013 -6.052 -4.025 6.340 2.796 -0.651 C7P YAS 14
YAS C8A C15 C 0 1 Y N N N N N -16.956 7.373 -6.420 -5.598 -1.411 -1.822 C8A YAS 15
YAS C9P C16 C 0 1 N N N N N N -16.416 -3.665 -3.623 4.634 4.430 -1.249 C9P YAS 16
YAS CAD C17 C 0 1 N N N N N N -18.547 -11.484 -8.472 12.027 -3.987 0.021 CAD YAS 17
YAS CAF C18 C 0 1 N N N N N N -19.770 -11.142 -9.332 13.120 -4.865 0.571 CAF YAS 18
YAS CAI C19 C 0 1 N N N N N N -21.779 -11.974 -10.652 14.434 -6.959 0.205 CAI YAS 19
YAS CAJ C20 C 0 1 N N N N N N -20.804 -12.259 -9.490 13.324 -6.067 -0.354 CAJ YAS 20
YAS CAP C21 C 0 1 N N R N N N -16.763 -2.178 -3.629 3.466 4.870 -2.095 CAP YAS 21
YAS CBP C22 C 0 1 N N N N N N -16.130 -1.396 -4.796 2.277 3.939 -1.846 CBP YAS 22
YAS CCP C23 C 0 1 N N N N N N -16.588 0.047 -4.662 1.969 3.895 -0.348 CCP YAS 23
YAS CDP C24 C 0 1 N N N N N N -16.541 -1.918 -6.165 1.054 4.461 -2.603 CDP YAS 24
YAS CEP C25 C 0 1 N N N N N N -14.601 -1.395 -4.734 2.619 2.532 -2.339 CEP YAS 25
YAS N1A N1 N 0 1 Y N N N N N -15.046 11.200 -7.652 -8.612 -2.672 -4.853 N1A YAS 26
YAS N3A N2 N 0 1 Y N N N N N -16.125 10.679 -5.675 -8.815 -1.054 -3.215 N3A YAS 27
YAS N4P N3 N 0 1 N N N N N N -17.087 -8.901 -5.767 8.645 -0.159 -0.582 N4P YAS 28
YAS N6A N4 N 0 1 N N N N N N -14.756 9.660 -9.490 -6.648 -3.943 -5.154 N6A YAS 29
YAS N7A N5 N 0 1 Y N N N N N -16.319 7.747 -7.530 -5.605 -2.294 -2.777 N7A YAS 30
YAS N8P N6 N 0 1 N N N N N N -17.391 -4.647 -4.070 5.283 3.285 -1.540 N8P YAS 31
YAS N9A N7 N 0 1 Y N N N N N -16.997 8.408 -5.585 -6.795 -0.759 -1.781 N9A YAS 32
YAS O1A O1 O 0 1 N N N N N N -19.467 2.956 -4.849 -2.803 2.802 2.765 O1A YAS 33
YAS O2A O2 O 0 1 N N N N N N -17.322 4.169 -4.633 -1.853 0.546 3.379 O2A YAS 34
YAS O2B O3 O 0 1 N N N N N N -19.743 8.387 -5.153 -8.667 -1.482 -0.104 O2B YAS 35
YAS O3A O4 O 0 1 N N N N N N -17.877 2.256 -2.983 -1.058 1.825 1.224 O3A YAS 36
YAS O3B O5 O 0 1 N N N N N N -20.465 8.021 -2.763 -6.981 -1.946 1.747 O3B YAS 37
YAS O4A O6 O 0 1 N N N N N N -15.862 2.016 -1.392 1.362 1.975 2.241 O4A YAS 38
YAS O4B O7 O 0 1 N N N N N N -17.252 7.153 -3.417 -5.999 0.844 -0.200 O4B YAS 39
YAS O5A O8 O 0 1 N N N N N N -15.371 2.810 -3.671 -0.091 4.025 1.998 O5A YAS 40
YAS O5B O9 O 0 1 N N N N N N -19.164 4.540 -2.805 -3.490 0.834 1.343 O5B YAS 41
YAS O5P O10 O 0 1 N N N N N N -14.973 -8.408 -4.994 8.287 1.612 0.706 O5P YAS 42
YAS O6A O11 O 0 1 N N N N N N -16.180 0.372 -3.368 0.859 3.026 -0.116 O6A YAS 43
YAS O7A O12 O 0 1 N N N N N N -21.074 9.740 -0.873 -6.157 -2.007 4.243 O7A YAS 44
YAS O8A O13 O 0 1 N N N N N N -22.718 8.064 -1.640 -8.615 -2.018 3.670 O8A YAS 45
YAS O9A O14 O 0 1 N N N N N N -20.724 7.376 -0.298 -7.307 -4.122 3.186 O9A YAS 46
YAS O9P O15 O 0 1 N N N N N N -15.361 -4.043 -3.237 4.989 5.106 -0.308 O9P YAS 47
YAS OAE O16 O 0 1 N N N N N N -18.546 -12.456 -7.777 11.465 -4.291 -1.011 OAE YAS 48
YAS OAP O17 O 0 1 N N N N N N -18.168 -2.070 -3.643 3.104 6.208 -1.748 OAP YAS 49
YAS P1A P1 P 0 1 N N N N N N -18.451 3.502 -3.874 -2.312 1.530 2.190 P1A YAS 50
YAS P2A P2 P 0 1 N N N N N N -16.278 1.922 -2.840 0.260 2.741 1.351 P2A YAS 51
YAS P3B P3 P 0 1 N N N N N N -21.262 8.316 -1.349 -7.294 -2.512 3.221 P3B YAS 52
YAS S1P S1 S 0 1 N N N N N N -17.089 -10.401 -8.500 11.577 -2.558 0.851 S1P YAS 53
YAS H1 H1 H 0 1 N N N N N N -16.914 9.271 -3.731 -7.717 1.092 -1.366 H1 YAS 54
YAS H2 H2 H 0 1 N N N N N N -15.286 12.539 -6.077 -10.313 -1.531 -4.556 H2 YAS 55
YAS H3 H3 H 0 1 N N N N N N -18.921 9.917 -3.892 -8.765 0.459 0.635 H3 YAS 56
YAS H4 H4 H 0 1 N N N N N N -15.857 -11.837 -6.989 9.477 -2.699 -0.311 H4 YAS 57
YAS H5 H5 H 0 1 N N N N N N -15.136 -10.194 -7.083 10.684 -1.778 -1.241 H5 YAS 58
YAS H6 H6 H 0 1 N N N N N N -18.644 8.513 -1.920 -7.237 0.037 2.314 H6 YAS 59
YAS H7 H7 H 0 1 N N N N N N -17.842 -10.854 -5.790 9.289 -0.823 1.300 H7 YAS 60
YAS H8 H8 H 0 1 N N N N N N -16.303 -10.633 -4.889 10.496 0.097 0.371 H8 YAS 61
YAS H9 H9 H 0 1 N N N N N N -18.913 6.385 -4.154 -5.137 -0.970 0.384 H9 YAS 62
YAS H10 H10 H 0 1 N N N N N N -17.405 5.250 -1.993 -5.246 1.466 2.229 H10 YAS 63
YAS H11 H11 H 0 1 N N N N N N -18.917 5.890 -1.265 -4.665 -0.138 2.737 H11 YAS 64
YAS H12 H12 H 0 1 N N N N N N -15.362 -5.951 -5.407 7.322 1.665 -2.199 H12 YAS 65
YAS H13 H13 H 0 1 N N N N N N -16.962 -6.235 -6.172 6.115 0.745 -1.269 H13 YAS 66
YAS H14 H14 H 0 1 N N N N N N -17.918 -6.661 -3.883 5.926 2.620 0.342 H14 YAS 67
YAS H15 H15 H 0 1 N N N N N N -16.328 -6.210 -3.179 7.134 3.540 -0.587 H15 YAS 68
YAS H16 H16 H 0 1 N N N N N N -17.370 6.394 -6.230 -4.767 -1.222 -1.159 H16 YAS 69
YAS H17 H17 H 0 1 N N N N N N -19.412 -10.869 -10.335 14.047 -4.295 0.635 H17 YAS 70
YAS H18 H18 H 0 1 N N N N N N -20.274 -10.278 -8.875 12.840 -5.215 1.565 H18 YAS 71
YAS H19 H19 H 0 1 N N N N N N -22.504 -12.797 -10.733 14.153 -7.309 1.198 H19 YAS 72
YAS H20 H20 H 0 1 N N N N N N -22.313 -11.032 -10.459 14.579 -7.815 -0.454 H20 YAS 73
YAS H21 H21 H 0 1 N N N N N N -21.214 -11.889 -11.592 15.361 -6.389 0.269 H21 YAS 74
YAS H22 H22 H 0 1 N N N N N N -21.379 -12.348 -8.556 12.397 -6.637 -0.418 H22 YAS 75
YAS H23 H23 H 0 1 N N N N N N -20.279 -13.205 -9.689 13.604 -5.717 -1.348 H23 YAS 76
YAS H24 H24 H 0 1 N N N N N N -16.378 -1.743 -2.695 3.745 4.830 -3.148 H24 YAS 77
YAS H25 H25 H 0 1 N N N N N N -16.098 0.691 -5.407 2.841 3.523 0.191 H25 YAS 78
YAS H26 H26 H 0 1 N N N N N N -17.680 0.129 -4.767 1.725 4.897 0.003 H26 YAS 79
YAS H27 H27 H 0 1 N N N N N N -17.638 -1.930 -6.239 0.186 3.849 -2.357 H27 YAS 80
YAS H28 H28 H 0 1 N N N N N N -16.128 -1.263 -6.946 0.863 5.495 -2.316 H28 YAS 81
YAS H29 H29 H 0 1 N N N N N N -16.153 -2.939 -6.300 1.242 4.411 -3.676 H29 YAS 82
YAS H30 H30 H 0 1 N N N N N N -14.274 -1.021 -3.753 1.740 1.893 -2.253 H30 YAS 83
YAS H31 H31 H 0 1 N N N N N N -14.228 -2.419 -4.879 2.935 2.578 -3.381 H31 YAS 84
YAS H32 H32 H 0 1 N N N N N N -14.202 -0.744 -5.526 3.427 2.121 -1.733 H32 YAS 85
YAS H33 H33 H 0 1 N N N N N N -17.972 -8.533 -6.051 8.412 -0.659 -1.380 H33 YAS 86
YAS H34 H34 H 0 1 N N N N N N -14.297 10.457 -9.882 -7.051 -4.424 -5.894 H34 YAS 87
YAS H35 H35 H 0 1 N N N N N N -14.110 8.899 -9.430 -5.741 -4.148 -4.879 H35 YAS 88
YAS H36 H36 H 0 1 N N N N N N -18.293 -4.366 -4.398 5.050 2.784 -2.338 H36 YAS 89
YAS H37 H37 H 0 1 N N N N N N -17.487 4.106 -5.566 -1.519 -0.309 3.075 H37 YAS 90
YAS H38 H38 H 0 1 N N N N N N -20.623 8.671 -4.936 -9.276 -1.374 -0.847 H38 YAS 91
YAS H39 H39 H 0 1 N N N N N N -15.124 2.609 -1.312 1.640 1.124 1.876 H39 YAS 92
YAS H40 H40 H 0 1 N N N N N N -21.915 10.182 -0.856 -5.263 -2.295 4.011 H40 YAS 93
YAS H41 H41 H 0 1 N N N N N N -21.416 6.791 -0.012 -7.490 -4.533 4.042 H41 YAS 94
YAS H42 H42 H 0 1 N N N N N N -18.531 -2.560 -2.915 2.844 6.318 -0.823 H42 YAS 95
#
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
YAS CAI CAJ SING N N 1
YAS CAJ CAF SING N N 2
YAS N6A C6A SING N N 3
YAS CAF CAD SING N N 4
YAS S1P CAD SING N N 5
YAS S1P C2P SING N N 6
YAS CAD OAE DOUB N N 7
YAS C6A N1A DOUB Y N 8
YAS C6A C5A SING Y N 9
YAS N1A C2A SING Y N 10
YAS N7A C5A SING Y N 11
YAS N7A C8A DOUB Y N 12
YAS C5A C4A DOUB Y N 13
YAS C2P C3P SING N N 14
YAS C2A N3A DOUB Y N 15
YAS C8A N9A SING Y N 16
YAS CDP CBP SING N N 17
YAS C4A N3A SING Y N 18
YAS C4A N9A SING Y N 19
YAS C3P N4P SING N N 20
YAS N4P C5P SING N N 21
YAS N9A C1B SING N N 22
YAS C5P C6P SING N N 23
YAS C5P O5P DOUB N N 24
YAS C6P C7P SING N N 25
YAS O2B C2B SING N N 26
YAS O1A P1A DOUB N N 27
YAS CBP CEP SING N N 28
YAS CBP CCP SING N N 29
YAS CBP CAP SING N N 30
YAS CCP O6A SING N N 31
YAS O2A P1A SING N N 32
YAS C1B C2B SING N N 33
YAS C1B O4B SING N N 34
YAS C2B C3B SING N N 35
YAS N8P C7P SING N N 36
YAS N8P C9P SING N N 37
YAS P1A O3A SING N N 38
YAS P1A O5B SING N N 39
YAS O5A P2A DOUB N N 40
YAS OAP CAP SING N N 41
YAS CAP C9P SING N N 42
YAS C9P O9P DOUB N N 43
YAS O4B C4B SING N N 44
YAS O6A P2A SING N N 45
YAS C4B C3B SING N N 46
YAS C4B C5B SING N N 47
YAS O3A P2A SING N N 48
YAS P2A O4A SING N N 49
YAS C3B O3B SING N N 50
YAS O5B C5B SING N N 51
YAS O3B P3B SING N N 52
YAS O8A P3B DOUB N N 53
YAS P3B O7A SING N N 54
YAS P3B O9A SING N N 55
YAS C1B H1 SING N N 56
YAS C2A H2 SING N N 57
YAS C2B H3 SING N N 58
YAS C2P H4 SING N N 59
YAS C2P H5 SING N N 60
YAS C3B H6 SING N N 61
YAS C3P H7 SING N N 62
YAS C3P H8 SING N N 63
YAS C4B H9 SING N N 64
YAS C5B H10 SING N N 65
YAS C5B H11 SING N N 66
YAS C6P H12 SING N N 67
YAS C6P H13 SING N N 68
YAS C7P H14 SING N N 69
YAS C7P H15 SING N N 70
YAS C8A H16 SING N N 71
YAS CAF H17 SING N N 72
YAS CAF H18 SING N N 73
YAS CAI H19 SING N N 74
YAS CAI H20 SING N N 75
YAS CAI H21 SING N N 76
YAS CAJ H22 SING N N 77
YAS CAJ H23 SING N N 78
YAS CAP H24 SING N N 79
YAS CCP H25 SING N N 80
YAS CCP H26 SING N N 81
YAS CDP H27 SING N N 82
YAS CDP H28 SING N N 83
YAS CDP H29 SING N N 84
YAS CEP H30 SING N N 85
YAS CEP H31 SING N N 86
YAS CEP H32 SING N N 87
YAS N4P H33 SING N N 88
YAS N6A H34 SING N N 89
YAS N6A H35 SING N N 90
YAS N8P H36 SING N N 91
YAS O2A H37 SING N N 92
YAS O2B H38 SING N N 93
YAS O4A H39 SING N N 94
YAS O7A H40 SING N N 95
YAS O9A H41 SING N N 96
YAS OAP H42 SING N N 97
#
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
YAS InChI InChI 1.03 InChI=1S/C25H42N7O17P3S/c1-4-5-16(34)53-9-8-27-15(33)6-7-28-23(37)20(36)25(2,3)11-46-52(43,44)49-51(41,42)45-10-14-19(48-50(38,39)40)18(35)24(47-14)32-13-31-17-21(26)29-12-30-22(17)32/h12-14,18-20,24,35-36H,4-11H2,1-3H3,(H,27,33)(H,28,37)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/t14-,18-,19-,20-,24+/m0/s1
YAS InChIKey InChI 1.03 CRFNGMNYKDXRTN-JSFVJHESSA-N
YAS SMILES_CANONICAL CACTVS 3.385 CCCC(=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
YAS SMILES CACTVS 3.385 CCCC(=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
YAS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CCCC(=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
YAS SMILES "OpenEye OEToolkits" 2.0.6 CCCC(=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
#
_pdbx_chem_comp_identifier.comp_id YAS
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier
"~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{R},4~{S},5~{R})-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] butanethioate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YAS 'Create component' 2018-12-06 RCSB
YAS 'Initial release' 2020-03-18 RCSB
YAS 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id YAS
_pdbx_chem_comp_synonyms.name Butyryl-CoA
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id YAS
_pdbe_chem_comp_synonyms.name Butyryl-CoA
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
YAS C1B C 7.483 -0.434 1
YAS C2A C 3.000 -2.317 2
YAS C2B C 6.604 0.781 3
YAS C2P C 30.957 3.052 4
YAS C3B C 7.487 1.993 5
YAS C3P C 29.588 3.664 6
YAS C4A C 5.598 -2.317 7
YAS C4B C 8.913 1.527 8
YAS C5A C 5.598 -3.817 9
YAS C5B C 10.129 2.407 10
YAS C5P C 27.004 3.397 11
YAS C6A C 4.299 -4.567 12
YAS C6P C 25.788 2.517 13
YAS C7P C 24.419 3.130 14
YAS C8A C 7.893 -3.067 15
YAS C9P C 21.835 2.863 16
YAS CAD C 33.541 3.319 17
YAS CAF C 34.757 4.198 18
YAS CAI C 37.341 4.465 19
YAS CAJ C 36.126 3.586 20
YAS CAP C 20.620 1.983 21
YAS CBP C 19.251 2.596 22
YAS CCP C 17.881 3.208 23
YAS CDP C 19.863 3.965 24
YAS CEP C 18.638 1.226 25
YAS N1A N 3.000 -3.817 26
YAS N3A N 4.299 -1.567 27
YAS N4P N 28.373 2.785 28
YAS N6A N 4.299 -6.067 29
YAS N7A N 7.018 -4.274 30
YAS N8P N 23.204 2.250 31
YAS N9A N 7.018 -1.860 32
YAS O1A O 13.592 1.459 33
YAS O2A O 11.833 3.889 34
YAS O2B O 5.104 0.784 35
YAS O3A O 13.928 3.554 36
YAS O3B O 7.027 3.421 37
YAS O4A O 14.684 1.572 38
YAS O4B O 8.911 0.027 39
YAS O5A O 15.909 4.310 40
YAS O5B O 11.498 1.794 41
YAS O5P O 26.849 4.889 42
YAS O6A O 16.666 2.329 43
YAS O7A O 6.919 5.539 44
YAS O8A O 9.038 5.647 45
YAS O9A O 9.145 3.528 46
YAS O9P O 21.681 4.355 47
YAS OAE O 33.696 1.827 48
YAS OAP O 20.774 0.491 49
YAS P1A P 12.713 2.674 50
YAS P2A P 15.297 2.941 51
YAS P3B P 8.032 4.534 52
YAS S1P S 32.172 3.931 53
#
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
YAS CAI CAJ SINGLE NONE 1
YAS CAJ CAF SINGLE NONE 2
YAS N6A C6A SINGLE NONE 3
YAS CAF CAD SINGLE NONE 4
YAS S1P CAD SINGLE NONE 5
YAS S1P C2P SINGLE NONE 6
YAS CAD OAE DOUBLE NONE 7
YAS C6A N1A SINGLE NONE 8
YAS C6A C5A DOUBLE NONE 9
YAS N1A C2A DOUBLE NONE 10
YAS N7A C5A SINGLE NONE 11
YAS N7A C8A DOUBLE NONE 12
YAS C5A C4A SINGLE NONE 13
YAS C2P C3P SINGLE NONE 14
YAS C2A N3A SINGLE NONE 15
YAS C8A N9A SINGLE NONE 16
YAS CDP CBP SINGLE NONE 17
YAS C4A N3A DOUBLE NONE 18
YAS C4A N9A SINGLE NONE 19
YAS C3P N4P SINGLE NONE 20
YAS N4P C5P SINGLE NONE 21
YAS C1B N9A SINGLE BEGINWEDGE 22
YAS C5P C6P SINGLE NONE 23
YAS C5P O5P DOUBLE NONE 24
YAS C6P C7P SINGLE NONE 25
YAS C2B O2B SINGLE BEGINWEDGE 26
YAS O1A P1A DOUBLE NONE 27
YAS CBP CEP SINGLE NONE 28
YAS CBP CCP SINGLE NONE 29
YAS CBP CAP SINGLE NONE 30
YAS CCP O6A SINGLE NONE 31
YAS P1A O2A SINGLE BEGINDASH 32
YAS C1B C2B SINGLE NONE 33
YAS C1B O4B SINGLE NONE 34
YAS C2B C3B SINGLE NONE 35
YAS N8P C7P SINGLE NONE 36
YAS N8P C9P SINGLE NONE 37
YAS P1A O3A SINGLE NONE 38
YAS P1A O5B SINGLE NONE 39
YAS O5A P2A DOUBLE NONE 40
YAS CAP OAP SINGLE BEGINDASH 41
YAS CAP C9P SINGLE NONE 42
YAS C9P O9P DOUBLE NONE 43
YAS O4B C4B SINGLE NONE 44
YAS O6A P2A SINGLE NONE 45
YAS C4B C3B SINGLE NONE 46
YAS C4B C5B SINGLE BEGINDASH 47
YAS O3A P2A SINGLE NONE 48
YAS P2A O4A SINGLE BEGINWEDGE 49
YAS C3B O3B SINGLE BEGINWEDGE 50
YAS O5B C5B SINGLE NONE 51
YAS O3B P3B SINGLE NONE 52
YAS O8A P3B DOUBLE NONE 53
YAS P3B O7A SINGLE NONE 54
YAS P3B O9A SINGLE NONE 55
#
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
YAS 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
YAS 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
YAS amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YAS imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
YAS 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
YAS 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
YAS pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
YAS 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
YAS C1B S1 1
YAS C2A S1 1
YAS C2B S1 1
YAS C3B S1 1
YAS C4A S1 1
YAS C4B S1 1
YAS C5A S1 1
YAS C6A S1 1
YAS C8A S1 1
YAS N1A S1 1
YAS N3A S1 1
YAS N7A S1 1
YAS N9A S1 1
YAS O4B S1 1
YAS N1A F1 1
YAS C6A F1 1
YAS C5A F1 1
YAS C4A F1 1
YAS N3A F1 1
YAS C2A F1 1
YAS N9A F1 1
YAS C8A F1 1
YAS N7A F1 1
YAS N6A F1 1
YAS N4P F2 1
YAS C5P F2 1
YAS O5P F2 1
YAS C6P F2 1
YAS N8P F2 2
YAS C9P F2 2
YAS O9P F2 2
YAS CAP F2 2
YAS C4A F3 1
YAS C5A F3 1
YAS N7A F3 1
YAS C8A F3 1
YAS N9A F3 1
YAS O2A F4 1
YAS P1A F4 1
YAS O1A F4 1
YAS O3A F4 1
YAS O5B F4 1
YAS O3A F4 2
YAS P2A F4 2
YAS O5A F4 2
YAS O6A F4 2
YAS O4A F4 2
YAS O3B F4 3
YAS P3B F4 3
YAS O8A F4 3
YAS O7A F4 3
YAS O9A F4 3
YAS N7A F5 1
YAS C8A F5 1
YAS N9A F5 1
YAS C4A F5 1
YAS C5A F5 1
YAS C6A F5 1
YAS N1A F5 1
YAS C2A F5 1
YAS N3A F5 1
YAS C5A F6 1
YAS C6A F6 1
YAS N1A F6 1
YAS C2A F6 1
YAS N3A F6 1
YAS C4A F6 1
YAS C2B F7 1
YAS C3B F7 1
YAS C4B F7 1
YAS O4B F7 1
YAS C1B F7 1
YAS C5B F7 1
YAS O5B F7 1
YAS O3B F7 1
YAS O2B F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YAS
_pdbe_chem_comp_rdkit_properties.exactmw 837.157
_pdbe_chem_comp_rdkit_properties.amw 837.632
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 24
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 31
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 23
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 53
_pdbe_chem_comp_rdkit_properties.NumAtoms 95
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 28
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.680
_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 365.274
_pdbe_chem_comp_rdkit_properties.tpsa 363.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.344
_pdbe_chem_comp_rdkit_properties.CrippenMR 178.976
_pdbe_chem_comp_rdkit_properties.chi0v 27.820
_pdbe_chem_comp_rdkit_properties.chi1v 17.219
_pdbe_chem_comp_rdkit_properties.chi2v 7.665
_pdbe_chem_comp_rdkit_properties.chi3v 7.665
_pdbe_chem_comp_rdkit_properties.chi4v 5.043
_pdbe_chem_comp_rdkit_properties.chi0n 66.321
_pdbe_chem_comp_rdkit_properties.chi1n 32.259
_pdbe_chem_comp_rdkit_properties.chi2n 4.548
_pdbe_chem_comp_rdkit_properties.chi3n 4.548
_pdbe_chem_comp_rdkit_properties.chi4n 2.678
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.440
_pdbe_chem_comp_rdkit_properties.kappa1 13.888
_pdbe_chem_comp_rdkit_properties.kappa2 18.936
_pdbe_chem_comp_rdkit_properties.kappa3 13.669
_pdbe_chem_comp_rdkit_properties.Phi 4.962
#
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
YAS UniChem PDBe YAS
YAS UniChem PubChem 145997877
#
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
YAS C1B 7.063 0.599 -1.002 ETKDGv3 1
YAS C2A 9.429 1.673 2.772 ETKDGv3 2
YAS C2B 7.377 -0.900 -1.077 ETKDGv3 3
YAS C2P -7.668 -0.362 -0.227 ETKDGv3 4
YAS C3B 6.861 -1.439 0.235 ETKDGv3 5
YAS C3P -8.342 1.008 -0.307 ETKDGv3 6
YAS C4A 8.938 1.611 0.478 ETKDGv3 7
YAS C4B 5.789 -0.413 0.607 ETKDGv3 8
YAS C5A 10.221 2.133 0.190 ETKDGv3 9
YAS C5B 4.388 -0.849 0.153 ETKDGv3 10
YAS C5P -6.562 2.490 -1.354 ETKDGv3 11
YAS C6A 11.075 2.404 1.175 ETKDGv3 12
YAS C6P -5.667 3.694 -1.235 ETKDGv3 13
YAS C7P -4.495 3.684 -2.224 ETKDGv3 14
YAS C8A 9.238 1.824 -1.719 ETKDGv3 15
YAS C9P -3.365 1.471 -2.794 ETKDGv3 16
YAS CAD -8.273 -1.505 2.126 ETKDGv3 17
YAS CAF -9.355 -0.772 2.866 ETKDGv3 18
YAS CAI -11.806 -0.175 2.899 ETKDGv3 19
YAS CAJ -10.717 -0.977 2.193 ETKDGv3 20
YAS CAP -2.396 0.376 -2.409 ETKDGv3 21
YAS CBP -3.070 -0.782 -1.597 ETKDGv3 22
YAS CCP -2.014 -1.867 -1.257 ETKDGv3 23
YAS CDP -3.664 -0.241 -0.276 ETKDGv3 24
YAS CEP -4.202 -1.445 -2.416 ETKDGv3 25
YAS N1A 10.627 2.153 2.527 ETKDGv3 26
YAS N3A 8.519 1.381 1.685 ETKDGv3 27
YAS N4P -7.354 2.083 -0.228 ETKDGv3 28
YAS N6A 12.382 2.917 0.922 ETKDGv3 29
YAS N7A 10.370 2.248 -1.219 ETKDGv3 30
YAS N8P -3.570 2.592 -1.921 ETKDGv3 31
YAS N9A 8.256 1.410 -0.745 ETKDGv3 32
YAS O1A 0.906 0.690 0.403 ETKDGv3 33
YAS O2A 1.938 -0.431 -1.724 ETKDGv3 34
YAS O2B 8.745 -1.172 -1.248 ETKDGv3 35
YAS O3A 1.518 -1.850 0.663 ETKDGv3 36
YAS O3B 7.883 -1.407 1.218 ETKDGv3 37
YAS O4A -0.470 -3.755 0.673 ETKDGv3 38
YAS O4B 6.110 0.828 0.014 ETKDGv3 39
YAS O5A 0.740 -3.054 -1.534 ETKDGv3 40
YAS O5B 3.455 0.138 0.526 ETKDGv3 41
YAS O5P -6.684 1.894 -2.459 ETKDGv3 42
YAS O6A -0.958 -1.298 -0.517 ETKDGv3 43
YAS O7A 9.585 -2.915 2.792 ETKDGv3 44
YAS O8A 8.827 -3.745 0.434 ETKDGv3 45
YAS O9A 7.014 -3.803 2.327 ETKDGv3 46
YAS O9P -4.001 1.386 -3.880 ETKDGv3 47
YAS OAE -8.312 -2.722 2.033 ETKDGv3 48
YAS OAP -1.785 -0.139 -3.567 ETKDGv3 49
YAS P1A 1.919 -0.346 -0.030 ETKDGv3 50
YAS P2A 0.220 -2.498 -0.226 ETKDGv3 51
YAS P3B 8.338 -2.993 1.652 ETKDGv3 52
YAS S1P -6.888 -0.612 1.409 ETKDGv3 53
YAS H1 6.622 0.923 -1.971 ETKDGv3 54
YAS H2 9.120 1.494 3.792 ETKDGv3 55
YAS H3 6.788 -1.361 -1.906 ETKDGv3 56
YAS H4 -8.414 -1.158 -0.437 ETKDGv3 57
YAS H5 -6.882 -0.436 -1.006 ETKDGv3 58
YAS H6 6.403 -2.447 0.080 ETKDGv3 59
YAS H7 -8.915 1.092 -1.255 ETKDGv3 60
YAS H8 -9.067 1.114 0.527 ETKDGv3 61
YAS H9 5.764 -0.284 1.712 ETKDGv3 62
YAS H10 4.145 -1.817 0.648 ETKDGv3 63
YAS H11 4.400 -0.987 -0.952 ETKDGv3 64
YAS H12 -6.280 4.602 -1.416 ETKDGv3 65
YAS H13 -5.266 3.758 -0.200 ETKDGv3 66
YAS H14 -3.946 4.645 -2.134 ETKDGv3 67
YAS H15 -4.872 3.623 -3.267 ETKDGv3 68
YAS H16 9.064 1.771 -2.786 ETKDGv3 69
YAS H17 -9.392 -1.147 3.912 ETKDGv3 70
YAS H18 -9.112 0.313 2.899 ETKDGv3 71
YAS H19 -12.780 -0.350 2.397 ETKDGv3 72
YAS H20 -11.890 -0.491 3.961 ETKDGv3 73
YAS H21 -11.574 0.911 2.856 ETKDGv3 74
YAS H22 -10.990 -2.055 2.221 ETKDGv3 75
YAS H23 -10.667 -0.657 1.130 ETKDGv3 76
YAS H24 -1.607 0.835 -1.767 ETKDGv3 77
YAS H25 -2.501 -2.678 -0.668 ETKDGv3 78
YAS H26 -1.635 -2.310 -2.207 ETKDGv3 79
YAS H27 -4.505 0.456 -0.472 ETKDGv3 80
YAS H28 -2.894 0.301 0.312 ETKDGv3 81
YAS H29 -4.053 -1.074 0.347 ETKDGv3 82
YAS H30 -4.648 -2.293 -1.852 ETKDGv3 83
YAS H31 -3.815 -1.837 -3.381 ETKDGv3 84
YAS H32 -5.016 -0.723 -2.634 ETKDGv3 85
YAS H33 -7.295 2.637 0.657 ETKDGv3 86
YAS H34 12.713 3.100 -0.052 ETKDGv3 87
YAS H35 13.027 3.116 1.719 ETKDGv3 88
YAS H36 -3.051 2.628 -1.015 ETKDGv3 89
YAS H37 2.219 0.472 -2.019 ETKDGv3 90
YAS H38 8.941 -1.033 -2.211 ETKDGv3 91
YAS H39 0.281 -4.372 0.864 ETKDGv3 92
YAS H40 9.218 -2.362 3.527 ETKDGv3 93
YAS H41 7.374 -4.680 2.616 ETKDGv3 94
YAS H42 -1.129 0.540 -3.875 ETKDGv3 95
#