data_T3D
#
_chem_comp.id T3D
_chem_comp.name
"(~{E})-6-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},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]ethylsulfanyl]-6-oxidanylidene-hex-3-enoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C27 H42 N7 O19 P3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-08-19
_chem_comp.pdbx_modified_date 2019-12-06
_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 893.644
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code T3D
_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 6SLB
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
T3D O1 OCD O 0 1 N N N N N N 2.685 8.723 23.365 15.901 6.448 -1.704 O1 T3D 1
T3D C1 CCC C 0 1 N N N N N N 2.493 9.366 22.303 15.469 5.582 -0.773 C1 T3D 2
T3D O2 OCE O 0 1 N N N N N N 2.937 9.116 21.145 14.445 5.803 -0.172 O2 T3D 3
T3D C2 CCB C 0 1 N N N N N N 1.587 10.549 22.424 16.261 4.334 -0.480 C2 T3D 4
T3D C3 CCA C 0 1 N N N N N N 0.259 9.873 22.162 15.565 3.539 0.595 C3 T3D 5
T3D C4 CBZ C 0 1 N N N N N N -0.467 9.138 23.297 15.251 2.285 0.383 C4 T3D 6
T3D C5 CBX C 0 1 N N N N N N -1.778 8.531 22.954 14.555 1.491 1.458 C5 T3D 7
T3D C6 CBW C 0 1 N N N N N N -2.396 7.708 24.136 13.282 0.904 0.905 C6 T3D 8
T3D O3 OBY O 0 1 N N N N N N -3.219 6.849 23.829 12.970 1.110 -0.249 O3 T3D 9
T3D S1 SBV S 0 1 N N N N N N -1.766 7.960 25.892 12.276 -0.055 1.905 S1 T3D 10
T3D C7 CBU C 0 1 N N N N N N -2.988 6.930 26.797 10.958 -0.456 0.731 C7 T3D 11
T3D C8 CBT C 0 1 N N N N N N -2.399 5.571 26.612 9.911 -1.333 1.421 C8 T3D 12
T3D N1 NBS N 0 1 N N N N N N -3.280 4.569 27.264 8.844 -1.658 0.472 N1 T3D 13
T3D C9 CBQ C 0 1 N N N N N N -3.332 4.377 28.585 7.806 -2.425 0.860 C9 T3D 14
T3D O4 OBR O 0 1 N N N N N N -2.854 5.192 29.392 7.756 -2.847 1.996 O4 T3D 15
T3D C10 CBP C 0 1 N N N N N N -4.164 3.174 29.061 6.708 -2.760 -0.116 C10 T3D 16
T3D C11 CBO C 0 1 N N N N N N -3.256 2.448 30.036 5.661 -3.636 0.573 C11 T3D 17
T3D N2 NBN N 0 1 N N N N N N -3.973 1.213 30.501 4.594 -3.961 -0.376 N2 T3D 18
T3D C12 CBL C 0 1 N N N N N N -4.971 1.193 31.385 3.557 -4.729 0.012 C12 T3D 19
T3D O5 OBM O 0 1 N N N N N N -5.309 2.178 32.039 3.552 -5.227 1.118 O5 T3D 20
T3D C13 CBJ C 0 1 N N R N N N -5.582 -0.193 31.637 2.403 -4.968 -0.927 C13 T3D 21
T3D O6 OBK O 0 1 N N N N N N -4.633 -1.232 31.220 2.754 -4.519 -2.237 O6 T3D 22
T3D C14 CBG C 0 1 N N N N N N -6.893 -0.402 30.852 1.177 -4.196 -0.435 C14 T3D 23
T3D C15 CBH C 0 1 N N N N N N -6.658 -0.092 29.330 0.711 -4.776 0.901 C15 T3D 24
T3D C16 CBI C 0 1 N N N N N N -8.038 0.502 31.342 1.542 -2.721 -0.251 C16 T3D 25
T3D C17 CBF C 0 1 N N N N N N -7.342 -1.857 30.943 0.051 -4.317 -1.464 C17 T3D 26
T3D O7 OBE O 0 1 N N N N N N -7.319 -2.362 32.330 -1.094 -3.596 -1.005 O7 T3D 27
T3D P1 PBB P 0 1 N N N N N N -7.340 -3.930 32.468 -2.468 -3.508 -1.840 P1 T3D 28
T3D O8 OBC O 0 1 N N N N N N -7.557 -4.248 33.913 -2.210 -2.711 -3.215 O8 T3D 29
T3D O9 OBD O 0 1 N N N N N N -8.257 -4.461 31.442 -2.948 -4.874 -2.145 O9 T3D 30
T3D O10 OBA O 0 1 N N N N N N -5.888 -4.449 32.042 -3.577 -2.731 -0.969 O10 T3D 31
T3D P2 PAX P 0 1 N N N N N N -4.478 -4.175 32.836 -5.185 -2.659 -1.013 P2 T3D 32
T3D O11 OAY O 0 1 N N N N N N -4.436 -5.186 33.929 -5.801 -3.962 -0.297 O11 T3D 33
T3D O12 OAZ O 0 1 N N N N N N -4.282 -2.777 33.196 -5.637 -2.609 -2.421 O12 T3D 34
T3D O13 O5* O 0 1 N N N N N N -3.425 -4.547 31.687 -5.683 -1.336 -0.242 O13 T3D 35
T3D C18 C5* C 0 1 N N N N N N -3.330 -5.862 31.205 -7.053 -0.933 -0.196 C18 T3D 36
T3D C19 C4* C 0 1 N N R N N N -2.060 -5.884 30.340 -7.177 0.360 0.614 C19 T3D 37
T3D O14 O4* O 0 1 N N N N N N -2.097 -4.961 29.119 -6.587 1.463 -0.106 O14 T3D 38
T3D C20 C3* C 0 1 N N S N N N -0.819 -5.432 31.146 -8.663 0.748 0.784 C20 T3D 39
T3D O15 O3* O 0 1 N N N N N N 0.336 -6.148 30.667 -9.148 0.325 2.060 O15 T3D 40
T3D P3 PAQ P 0 1 N N N N N N 0.960 -7.433 31.440 -10.374 -0.704 2.235 P3 T3D 41
T3D O16 OAS O 0 1 N N N N N N -0.055 -8.438 31.198 -11.723 -0.032 1.669 O16 T3D 42
T3D O17 OAT O 0 1 N N N N N N 2.205 -7.666 30.790 -10.087 -1.945 1.482 O17 T3D 43
T3D O18 OAR O 0 1 N N N N N N 1.083 -6.935 32.811 -10.562 -1.054 3.795 O18 T3D 44
T3D C21 C2* C 0 1 N N R N N N -0.742 -3.939 30.679 -8.661 2.290 0.686 C21 T3D 45
T3D O19 O2* O 0 1 N N N N N N 0.512 -3.263 30.849 -9.145 2.869 1.899 O19 T3D 46
T3D C22 C1* C 0 1 N N R N N N -1.036 -4.042 29.216 -7.175 2.651 0.468 C22 T3D 47
T3D N3 NAJ N 0 1 Y N N N N N -1.595 -2.752 28.719 -7.055 3.779 -0.458 N3 T3D 48
T3D C23 CAI C 0 1 Y N N N N N -2.752 -2.111 28.992 -6.908 3.700 -1.811 C23 T3D 49
T3D N4 NAH N 0 1 Y N N N N N -2.737 -0.917 28.388 -6.832 4.895 -2.321 N4 T3D 50
T3D C24 CAG C 0 1 Y N N N N N -1.567 -0.829 27.706 -6.925 5.814 -1.331 C24 T3D 51
T3D C25 CAF C 0 1 Y N N N N N -0.868 -1.933 27.972 -7.075 5.110 -0.124 C25 T3D 52
T3D N5 NAE N 0 1 Y N N N N N 0.375 -2.090 27.534 -7.190 5.791 1.011 N5 T3D 53
T3D C26 CAD C 0 1 Y N N N N N 1.083 -1.195 26.753 -7.164 7.107 1.010 C26 T3D 54
T3D N6 NAC N 0 1 Y N N N N N 0.284 -0.028 26.519 -7.025 7.812 -0.098 N6 T3D 55
T3D C27 CAB C 0 1 Y N N N N N -0.969 0.105 26.954 -6.911 7.219 -1.282 C27 T3D 56
T3D N7 NAA N 0 1 N N N N N N -1.636 1.223 26.635 -6.766 7.966 -2.437 N7 T3D 57
T3D H1 H1 H 0 1 N N N N N N 3.241 7.974 23.186 15.360 7.234 -1.857 H1 T3D 58
T3D H2 H2 H 0 1 N N N N N N 1.812 11.317 21.670 16.338 3.731 -1.385 H2 T3D 59
T3D H3 H3 H 0 1 N N N N N N 1.629 10.997 23.428 17.259 4.609 -0.140 H3 T3D 60
T3D H4 H4 H 0 1 N N N N N N -0.179 9.908 21.175 15.326 4.003 1.541 H4 T3D 61
T3D H5 H5 H 0 1 N N N N N N -0.048 9.066 24.290 15.490 1.821 -0.562 H5 T3D 62
T3D H6 H6 H 0 1 N N N N N N -2.477 9.336 22.683 15.209 0.687 1.796 H6 T3D 63
T3D H7 H7 H 0 1 N N N N N N -1.640 7.860 22.093 14.319 2.144 2.298 H7 T3D 64
T3D H8 H8 H 0 1 N N N N N N -3.042 7.207 27.860 10.489 0.464 0.383 H8 T3D 65
T3D H9 H9 H 0 1 N N N N N N -3.990 7.002 26.348 11.379 -0.994 -0.118 H9 T3D 66
T3D H10 H10 H 0 1 N N N N N N -2.318 5.347 25.538 10.380 -2.253 1.769 H10 T3D 67
T3D H11 H11 H 0 1 N N N N N N -1.400 5.537 27.070 9.490 -0.796 2.271 H11 T3D 68
T3D H12 H12 H 0 1 N N N N N N -3.867 4.007 26.682 8.884 -1.321 -0.437 H12 T3D 69
T3D H13 H13 H 0 1 N N N N N N -5.083 3.511 29.562 6.239 -1.839 -0.465 H13 T3D 70
T3D H14 H14 H 0 1 N N N N N N -4.426 2.523 28.214 7.129 -3.297 -0.966 H14 T3D 71
T3D H15 H15 H 0 1 N N N N N N -2.317 2.169 29.536 6.130 -4.557 0.921 H15 T3D 72
T3D H16 H16 H 0 1 N N N N N N -3.035 3.098 30.896 5.240 -3.099 1.423 H16 T3D 73
T3D H17 H17 H 0 1 N N N N N N -3.679 0.337 30.118 4.634 -3.624 -1.285 H17 T3D 74
T3D H18 H18 H 0 1 N N N N N N -5.795 -0.296 32.711 2.173 -6.033 -0.957 H18 T3D 75
T3D H19 H19 H 0 1 N N N N N N -4.480 -1.830 31.942 2.971 -3.578 -2.286 H19 T3D 76
T3D H20 H20 H 0 1 N N N N N N -6.331 0.952 29.214 0.524 -5.844 0.789 H20 T3D 77
T3D H21 H21 H 0 1 N N N N N N -5.883 -0.765 28.934 1.483 -4.620 1.655 H21 T3D 78
T3D H22 H22 H 0 1 N N N N N N -7.595 -0.246 28.776 -0.208 -4.278 1.214 H22 T3D 79
T3D H23 H23 H 0 1 N N N N N N -8.228 0.309 32.408 0.669 -2.171 0.099 H23 T3D 80
T3D H24 H24 H 0 1 N N N N N N -7.757 1.557 31.205 2.344 -2.635 0.482 H24 T3D 81
T3D H25 H25 H 0 1 N N N N N N -8.948 0.287 30.763 1.874 -2.308 -1.203 H25 T3D 82
T3D H26 H26 H 0 1 N N N N N N -8.368 -1.936 30.554 0.383 -3.904 -2.417 H26 T3D 83
T3D H27 H27 H 0 1 N N N N N N -6.669 -2.474 30.330 -0.210 -5.367 -1.595 H27 T3D 84
T3D H28 H28 H 0 1 N N N N N N -8.324 -4.801 34.004 -1.893 -1.806 -3.091 H28 T3D 85
T3D H29 H29 H 0 1 N N N N N N -4.278 -4.750 34.758 -5.545 -4.059 0.631 H29 T3D 86
T3D H30 H30 H 0 1 N N N N N N -4.213 -6.116 30.600 -7.416 -0.762 -1.209 H30 T3D 87
T3D H31 H31 H 0 1 N N N N N N -3.241 -6.573 32.039 -7.647 -1.715 0.276 H31 T3D 88
T3D H32 H32 H 0 1 N N N N N N -1.892 -6.915 29.994 -6.702 0.243 1.588 H32 T3D 89
T3D H33 H33 H 0 1 N N N N N N -0.976 -5.515 32.232 -9.264 0.315 -0.015 H33 T3D 90
T3D H34 H34 H 0 1 N N N N N N 0.294 -9.110 30.624 -11.972 0.788 2.117 H34 T3D 91
T3D H35 H35 H 0 1 N N N N N N 2.002 -6.851 33.037 -11.285 -1.670 3.975 H35 T3D 92
T3D H36 H36 H 0 1 N N N N N N -1.547 -3.377 31.174 -9.264 2.619 -0.161 H36 T3D 93
T3D H37 H37 H 0 1 N N N N N N 0.710 -3.191 31.775 -9.165 3.836 1.892 H37 T3D 94
T3D H38 H38 H 0 1 N N N N N N -0.147 -4.347 28.644 -6.699 2.888 1.420 H38 T3D 95
T3D H39 H39 H 0 1 N N N N N N -3.557 -2.499 29.598 -6.861 2.781 -2.376 H39 T3D 96
T3D H40 H40 H 0 1 N N N N N N 2.083 -1.351 26.377 -7.260 7.629 1.950 H40 T3D 97
T3D H41 H41 H 0 1 N N N N N N -1.048 1.817 26.086 -6.746 8.935 -2.389 H41 T3D 98
T3D H42 H42 H 0 1 N N N N N N -2.453 0.985 26.110 -6.684 7.521 -3.295 H42 T3D 99
#
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
T3D O2 C1 DOUB N N 1
T3D C3 C2 SING N N 2
T3D C3 C4 DOUB N E 3
T3D C1 C2 SING N N 4
T3D C1 O1 SING N N 5
T3D C5 C4 SING N N 6
T3D C5 C6 SING N N 7
T3D O3 C6 DOUB N N 8
T3D C6 S1 SING N N 9
T3D S1 C7 SING N N 10
T3D N6 C26 DOUB Y N 11
T3D N6 C27 SING Y N 12
T3D C8 C7 SING N N 13
T3D C8 N1 SING N N 14
T3D N7 C27 SING N N 15
T3D C26 N5 SING Y N 16
T3D C27 C24 DOUB Y N 17
T3D N1 C9 SING N N 18
T3D N5 C25 DOUB Y N 19
T3D C24 C25 SING Y N 20
T3D C24 N4 SING Y N 21
T3D C25 N3 SING Y N 22
T3D N4 C23 DOUB Y N 23
T3D C9 C10 SING N N 24
T3D C9 O4 DOUB N N 25
T3D N3 C23 SING Y N 26
T3D N3 C22 SING N N 27
T3D C10 C11 SING N N 28
T3D O14 C22 SING N N 29
T3D O14 C19 SING N N 30
T3D C22 C21 SING N N 31
T3D C15 C14 SING N N 32
T3D C11 N2 SING N N 33
T3D C19 C20 SING N N 34
T3D C19 C18 SING N N 35
T3D N2 C12 SING N N 36
T3D O15 C20 SING N N 37
T3D O15 P3 SING N N 38
T3D C21 O19 SING N N 39
T3D C21 C20 SING N N 40
T3D O17 P3 DOUB N N 41
T3D C14 C17 SING N N 42
T3D C14 C16 SING N N 43
T3D C14 C13 SING N N 44
T3D C17 O7 SING N N 45
T3D O16 P3 SING N N 46
T3D C18 O13 SING N N 47
T3D O6 C13 SING N N 48
T3D C12 C13 SING N N 49
T3D C12 O5 DOUB N N 50
T3D P3 O18 SING N N 51
T3D O9 P1 DOUB N N 52
T3D O13 P2 SING N N 53
T3D O10 P1 SING N N 54
T3D O10 P2 SING N N 55
T3D O7 P1 SING N N 56
T3D P1 O8 SING N N 57
T3D P2 O12 DOUB N N 58
T3D P2 O11 SING N N 59
T3D O1 H1 SING N N 60
T3D C2 H2 SING N N 61
T3D C2 H3 SING N N 62
T3D C3 H4 SING N N 63
T3D C4 H5 SING N N 64
T3D C5 H6 SING N N 65
T3D C5 H7 SING N N 66
T3D C7 H8 SING N N 67
T3D C7 H9 SING N N 68
T3D C8 H10 SING N N 69
T3D C8 H11 SING N N 70
T3D N1 H12 SING N N 71
T3D C10 H13 SING N N 72
T3D C10 H14 SING N N 73
T3D C11 H15 SING N N 74
T3D C11 H16 SING N N 75
T3D N2 H17 SING N N 76
T3D C13 H18 SING N N 77
T3D O6 H19 SING N N 78
T3D C15 H20 SING N N 79
T3D C15 H21 SING N N 80
T3D C15 H22 SING N N 81
T3D C16 H23 SING N N 82
T3D C16 H24 SING N N 83
T3D C16 H25 SING N N 84
T3D C17 H26 SING N N 85
T3D C17 H27 SING N N 86
T3D O8 H28 SING N N 87
T3D O11 H29 SING N N 88
T3D C18 H30 SING N N 89
T3D C18 H31 SING N N 90
T3D C19 H32 SING N N 91
T3D C20 H33 SING N N 92
T3D O16 H34 SING N N 93
T3D O18 H35 SING N N 94
T3D C21 H36 SING N N 95
T3D O19 H37 SING N N 96
T3D C22 H38 SING N N 97
T3D C23 H39 SING N N 98
T3D C26 H40 SING N N 99
T3D N7 H41 SING N N 100
T3D N7 H42 SING N N 101
#
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
T3D InChI InChI 1.03 InChI=1S/C27H42N7O19P3S/c1-27(2,22(40)25(41)30-8-7-16(35)29-9-10-57-18(38)6-4-3-5-17(36)37)12-50-56(47,48)53-55(45,46)49-11-15-21(52-54(42,43)44)20(39)26(51-15)34-14-33-19-23(28)31-13-32-24(19)34/h3-4,13-15,20-22,26,39-40H,5-12H2,1-2H3,(H,29,35)(H,30,41)(H,36,37)(H,45,46)(H,47,48)(H2,28,31,32)(H2,42,43,44)/b4-3+/t15-,20-,21-,22+,26-/m1/s1
T3D InChIKey InChI 1.03 VYSXESTVCZRDBA-ZPJAMBCCSA-N
T3D SMILES_CANONICAL CACTVS 3.385 CC(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)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)C/C=C/CC(O)=O
T3D SMILES CACTVS 3.385 CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CC=CCC(O)=O
T3D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)C/C=C/CC(=O)O)O
T3D SMILES "OpenEye OEToolkits" 2.0.7 CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CC=CCC(=O)O)O
#
_pdbx_chem_comp_identifier.comp_id T3D
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
"(~{E})-6-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},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]ethylsulfanyl]-6-oxidanylidene-hex-3-enoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
T3D 'Create component' 2019-08-19 EBI
T3D 'Initial release' 2019-12-11 RCSB
#
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
T3D O1 O 39.771 6.225 1
T3D C1 C 39.925 4.732 2
T3D O2 O 41.294 4.120 3
T3D C2 C 38.710 3.853 4
T3D C3 C 37.341 4.465 5
T3D C4 C 36.126 3.586 6
T3D C5 C 34.757 4.198 7
T3D C6 C 33.541 3.319 8
T3D O3 O 33.696 1.827 9
T3D S1 S 32.172 3.931 10
T3D C7 C 30.957 3.052 11
T3D C8 C 29.588 3.664 12
T3D N1 N 28.373 2.785 13
T3D C9 C 27.004 3.397 14
T3D O4 O 26.849 4.889 15
T3D C10 C 25.788 2.517 16
T3D C11 C 24.419 3.130 17
T3D N2 N 23.204 2.250 18
T3D C12 C 21.835 2.863 19
T3D O5 O 21.681 4.355 20
T3D C13 C 20.620 1.983 21
T3D O6 O 20.774 0.491 22
T3D C14 C 19.251 2.596 23
T3D C15 C 19.863 3.965 24
T3D C16 C 18.638 1.226 25
T3D C17 C 17.881 3.208 26
T3D O7 O 16.666 2.329 27
T3D P1 P 15.297 2.941 28
T3D O8 O 14.684 1.572 29
T3D O9 O 15.909 4.310 30
T3D O10 O 13.928 3.554 31
T3D P2 P 12.713 2.674 32
T3D O11 O 11.833 3.889 33
T3D O12 O 13.592 1.459 34
T3D O13 O 11.498 1.794 35
T3D C18 C 10.129 2.407 36
T3D C19 C 8.913 1.527 37
T3D O14 O 8.911 0.027 38
T3D C20 C 7.487 1.993 39
T3D O15 O 7.027 3.421 40
T3D P3 P 8.032 4.534 41
T3D O16 O 6.919 5.539 42
T3D O17 O 9.038 5.647 43
T3D O18 O 9.145 3.528 44
T3D C21 C 6.604 0.781 45
T3D O19 O 5.104 0.784 46
T3D C22 C 7.483 -0.434 47
T3D N3 N 7.018 -1.860 48
T3D C23 C 7.893 -3.067 49
T3D N4 N 7.018 -4.274 50
T3D C24 C 5.598 -3.817 51
T3D C25 C 5.598 -2.317 52
T3D N5 N 4.299 -1.567 53
T3D C26 C 3.000 -2.317 54
T3D N6 N 3.000 -3.817 55
T3D C27 C 4.299 -4.567 56
T3D N7 N 4.299 -6.067 57
#
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
T3D O2 C1 DOUBLE NONE 1
T3D C3 C2 SINGLE ENDDOWNRIGHT 2
T3D C3 C4 DOUBLE NONE 3
T3D C1 C2 SINGLE NONE 4
T3D C1 O1 SINGLE NONE 5
T3D C5 C4 SINGLE ENDDOWNRIGHT 6
T3D C5 C6 SINGLE NONE 7
T3D O3 C6 DOUBLE NONE 8
T3D C6 S1 SINGLE NONE 9
T3D S1 C7 SINGLE NONE 10
T3D N6 C26 DOUBLE NONE 11
T3D N6 C27 SINGLE NONE 12
T3D C8 C7 SINGLE NONE 13
T3D C8 N1 SINGLE NONE 14
T3D N7 C27 SINGLE NONE 15
T3D C26 N5 SINGLE NONE 16
T3D C27 C24 DOUBLE NONE 17
T3D N1 C9 SINGLE NONE 18
T3D N5 C25 DOUBLE NONE 19
T3D C24 C25 SINGLE NONE 20
T3D C24 N4 SINGLE NONE 21
T3D C25 N3 SINGLE NONE 22
T3D N4 C23 DOUBLE NONE 23
T3D C9 C10 SINGLE NONE 24
T3D C9 O4 DOUBLE NONE 25
T3D N3 C23 SINGLE NONE 26
T3D C22 N3 SINGLE BEGINWEDGE 27
T3D C10 C11 SINGLE NONE 28
T3D O14 C22 SINGLE NONE 29
T3D O14 C19 SINGLE NONE 30
T3D C22 C21 SINGLE NONE 31
T3D C15 C14 SINGLE NONE 32
T3D C11 N2 SINGLE NONE 33
T3D C19 C20 SINGLE NONE 34
T3D C19 C18 SINGLE BEGINWEDGE 35
T3D N2 C12 SINGLE NONE 36
T3D C20 O15 SINGLE BEGINDASH 37
T3D O15 P3 SINGLE NONE 38
T3D C21 O19 SINGLE BEGINDASH 39
T3D C21 C20 SINGLE NONE 40
T3D O17 P3 DOUBLE NONE 41
T3D C14 C17 SINGLE NONE 42
T3D C14 C16 SINGLE NONE 43
T3D C14 C13 SINGLE NONE 44
T3D C17 O7 SINGLE NONE 45
T3D O16 P3 SINGLE NONE 46
T3D C18 O13 SINGLE NONE 47
T3D C13 O6 SINGLE BEGINDASH 48
T3D C12 C13 SINGLE NONE 49
T3D C12 O5 DOUBLE NONE 50
T3D P3 O18 SINGLE NONE 51
T3D O9 P1 DOUBLE NONE 52
T3D O13 P2 SINGLE NONE 53
T3D O10 P1 SINGLE NONE 54
T3D O10 P2 SINGLE NONE 55
T3D O7 P1 SINGLE NONE 56
T3D P1 O8 SINGLE BEGINWEDGE 57
T3D P2 O12 DOUBLE NONE 58
T3D P2 O11 SINGLE BEGINWEDGE 59
#
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
T3D 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
T3D 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
T3D amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
T3D imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
T3D 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
T3D 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
T3D pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
T3D 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
T3D C19 S1 1
T3D O14 S1 1
T3D C20 S1 1
T3D C21 S1 1
T3D C22 S1 1
T3D N3 S1 1
T3D C23 S1 1
T3D N4 S1 1
T3D C24 S1 1
T3D C25 S1 1
T3D N5 S1 1
T3D C26 S1 1
T3D N6 S1 1
T3D C27 S1 1
T3D N6 F1 1
T3D C27 F1 1
T3D C24 F1 1
T3D C25 F1 1
T3D N5 F1 1
T3D C26 F1 1
T3D N3 F1 1
T3D C23 F1 1
T3D N4 F1 1
T3D N7 F1 1
T3D N1 F2 1
T3D C9 F2 1
T3D O4 F2 1
T3D C10 F2 1
T3D N2 F2 2
T3D C12 F2 2
T3D O5 F2 2
T3D C13 F2 2
T3D C24 F3 1
T3D C25 F3 1
T3D N3 F3 1
T3D C23 F3 1
T3D N4 F3 1
T3D O7 F4 1
T3D P1 F4 1
T3D O9 F4 1
T3D O10 F4 1
T3D O8 F4 1
T3D O10 F4 2
T3D P2 F4 2
T3D O12 F4 2
T3D O13 F4 2
T3D O11 F4 2
T3D O15 F4 3
T3D P3 F4 3
T3D O17 F4 3
T3D O16 F4 3
T3D O18 F4 3
T3D N4 F5 1
T3D C23 F5 1
T3D N3 F5 1
T3D C25 F5 1
T3D C24 F5 1
T3D C27 F5 1
T3D N6 F5 1
T3D C26 F5 1
T3D N5 F5 1
T3D C24 F6 1
T3D C27 F6 1
T3D N6 F6 1
T3D C26 F6 1
T3D N5 F6 1
T3D C25 F6 1
T3D C21 F7 1
T3D C20 F7 1
T3D C19 F7 1
T3D O14 F7 1
T3D C22 F7 1
T3D C18 F7 1
T3D O13 F7 1
T3D O15 F7 1
T3D O19 F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id T3D
_pdbe_chem_comp_rdkit_properties.exactmw 893.147
_pdbe_chem_comp_rdkit_properties.amw 893.652
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 26
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 11
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 32
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 25
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 57
_pdbe_chem_comp_rdkit_properties.NumAtoms 99
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 30
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.593
_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 386.357
_pdbe_chem_comp_rdkit_properties.tpsa 400.930
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.723
_pdbe_chem_comp_rdkit_properties.CrippenMR 190.078
_pdbe_chem_comp_rdkit_properties.chi0v 29.637
_pdbe_chem_comp_rdkit_properties.chi1v 18.127
_pdbe_chem_comp_rdkit_properties.chi2v 7.892
_pdbe_chem_comp_rdkit_properties.chi3v 7.892
_pdbe_chem_comp_rdkit_properties.chi4v 5.157
_pdbe_chem_comp_rdkit_properties.chi0n 68.137
_pdbe_chem_comp_rdkit_properties.chi1n 33.076
_pdbe_chem_comp_rdkit_properties.chi2n 4.775
_pdbe_chem_comp_rdkit_properties.chi3n 4.775
_pdbe_chem_comp_rdkit_properties.chi4n 2.792
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.230
_pdbe_chem_comp_rdkit_properties.kappa1 15.664
_pdbe_chem_comp_rdkit_properties.kappa2 20.644
_pdbe_chem_comp_rdkit_properties.kappa3 15.469
_pdbe_chem_comp_rdkit_properties.Phi 5.673
#
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
T3D UniChem PDBe T3D
T3D UniChem PubChem 145946137
T3D UniChem BRENDA 152162
T3D UniChem BRENDA 162149
#
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
T3D O1 8.820 1.709 -0.725 ETKDGv3 1
T3D C1 7.859 2.538 -0.156 ETKDGv3 2
T3D O2 7.831 3.764 -0.448 ETKDGv3 3
T3D C2 6.833 1.964 0.769 ETKDGv3 4
T3D C3 5.740 1.293 -0.012 ETKDGv3 5
T3D C4 4.842 2.003 -0.712 ETKDGv3 6
T3D C5 3.735 1.336 -1.477 ETKDGv3 7
T3D C6 4.262 0.660 -2.709 ETKDGv3 8
T3D O3 4.924 -0.361 -2.612 ETKDGv3 9
T3D S1 3.935 1.350 -4.337 ETKDGv3 10
T3D C7 2.267 0.618 -4.505 ETKDGv3 11
T3D C8 2.308 -0.725 -5.237 ETKDGv3 12
T3D N1 2.979 -1.751 -4.440 ETKDGv3 13
T3D C9 2.368 -2.371 -3.299 ETKDGv3 14
T3D O4 1.243 -1.975 -2.889 ETKDGv3 15
T3D C10 3.104 -3.459 -2.563 ETKDGv3 16
T3D C11 2.167 -4.427 -1.826 ETKDGv3 17
T3D N2 1.657 -3.829 -0.591 ETKDGv3 18
T3D C12 2.466 -3.721 0.593 ETKDGv3 19
T3D O5 3.657 -4.138 0.575 ETKDGv3 20
T3D C13 1.932 -3.104 1.870 ETKDGv3 21
T3D O6 0.655 -3.610 2.181 ETKDGv3 22
T3D C14 2.002 -1.534 1.911 ETKDGv3 23
T3D C15 1.189 -0.883 0.768 ETKDGv3 24
T3D C16 3.478 -1.086 1.777 ETKDGv3 25
T3D C17 1.449 -1.043 3.276 ETKDGv3 26
T3D O7 1.596 0.355 3.396 ETKDGv3 27
T3D P1 1.003 0.836 4.923 ETKDGv3 28
T3D O8 1.619 -0.175 6.134 ETKDGv3 29
T3D O9 1.463 2.248 5.211 ETKDGv3 30
T3D O10 -0.697 0.768 4.968 ETKDGv3 31
T3D P2 -1.310 1.635 3.633 ETKDGv3 32
T3D O11 -0.221 2.811 3.069 ETKDGv3 33
T3D O12 -2.583 2.322 4.076 ETKDGv3 34
T3D O13 -1.682 0.530 2.386 ETKDGv3 35
T3D C18 -2.051 1.259 1.238 ETKDGv3 36
T3D C19 -2.690 0.311 0.214 ETKDGv3 37
T3D O14 -3.812 -0.318 0.799 ETKDGv3 38
T3D C20 -3.129 1.064 -1.050 ETKDGv3 39
T3D O15 -2.943 0.243 -2.189 ETKDGv3 40
T3D P3 -1.445 0.612 -2.921 ETKDGv3 41
T3D O16 -0.197 0.548 -1.779 ETKDGv3 42
T3D O17 -1.171 -0.402 -4.008 ETKDGv3 43
T3D O18 -1.515 2.156 -3.611 ETKDGv3 44
T3D C21 -4.601 1.262 -0.802 ETKDGv3 45
T3D O19 -5.333 1.268 -2.001 ETKDGv3 46
T3D C22 -4.956 0.066 0.071 ETKDGv3 47
T3D N3 -6.042 0.391 0.993 ETKDGv3 48
T3D C23 -5.955 1.233 2.163 ETKDGv3 49
T3D N4 -7.095 1.720 2.582 ETKDGv3 50
T3D C24 -8.067 1.224 1.672 ETKDGv3 51
T3D C25 -7.423 0.427 0.696 ETKDGv3 52
T3D N5 -8.034 -0.059 -0.341 ETKDGv3 53
T3D C26 -9.454 0.193 -0.455 ETKDGv3 54
T3D N6 -10.075 0.926 0.441 ETKDGv3 55
T3D C27 -9.366 1.499 1.565 ETKDGv3 56
T3D N7 -10.039 2.343 2.499 ETKDGv3 57
T3D H1 9.513 2.080 -1.365 ETKDGv3 58
T3D H2 6.406 2.757 1.420 ETKDGv3 59
T3D H3 7.324 1.213 1.424 ETKDGv3 60
T3D H4 5.679 0.209 0.008 ETKDGv3 61
T3D H5 4.896 3.088 -0.716 ETKDGv3 62
T3D H6 3.212 0.598 -0.836 ETKDGv3 63
T3D H7 2.993 2.109 -1.771 ETKDGv3 64
T3D H8 1.773 0.515 -3.518 ETKDGv3 65
T3D H9 1.652 1.322 -5.104 ETKDGv3 66
T3D H10 1.273 -1.056 -5.471 ETKDGv3 67
T3D H11 2.844 -0.597 -6.202 ETKDGv3 68
T3D H12 3.910 -2.096 -4.765 ETKDGv3 69
T3D H13 3.695 -4.045 -3.299 ETKDGv3 70
T3D H14 3.821 -2.994 -1.854 ETKDGv3 71
T3D H15 1.317 -4.706 -2.487 ETKDGv3 72
T3D H16 2.713 -5.365 -1.584 ETKDGv3 73
T3D H17 0.658 -3.528 -0.573 ETKDGv3 74
T3D H18 2.596 -3.469 2.686 ETKDGv3 75
T3D H19 0.000 -3.240 1.539 ETKDGv3 76
T3D H20 0.116 -1.145 0.836 ETKDGv3 77
T3D H21 1.261 0.225 0.817 ETKDGv3 78
T3D H22 1.573 -1.195 -0.224 ETKDGv3 79
T3D H23 3.568 0.021 1.827 ETKDGv3 80
T3D H24 4.097 -1.521 2.590 ETKDGv3 81
T3D H25 3.902 -1.408 0.803 ETKDGv3 82
T3D H26 0.374 -1.322 3.358 ETKDGv3 83
T3D H27 2.015 -1.562 4.083 ETKDGv3 84
T3D H28 1.155 0.109 6.961 ETKDGv3 85
T3D H29 -0.782 3.493 2.620 ETKDGv3 86
T3D H30 -2.793 2.057 1.474 ETKDGv3 87
T3D H31 -1.146 1.719 0.784 ETKDGv3 88
T3D H32 -1.950 -0.473 -0.049 ETKDGv3 89
T3D H33 -2.652 2.069 -1.151 ETKDGv3 90
T3D H34 -0.052 1.487 -1.501 ETKDGv3 91
T3D H35 -0.605 2.315 -3.969 ETKDGv3 92
T3D H36 -4.751 2.219 -0.245 ETKDGv3 93
T3D H37 -6.226 1.642 -1.784 ETKDGv3 94
T3D H38 -5.263 -0.793 -0.567 ETKDGv3 95
T3D H39 -5.018 1.467 2.650 ETKDGv3 96
T3D H40 -10.007 -0.217 -1.289 ETKDGv3 97
T3D H41 -9.534 2.766 3.309 ETKDGv3 98
T3D H42 -11.056 2.546 2.378 ETKDGv3 99
#