data_TXD
#
_chem_comp.id TXD
_chem_comp.name "1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H31 N7 O14 P2"
_chem_comp.mon_nstd_parent_comp_id A
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-02-15
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 667.457
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code TXD
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_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
TXD O7N O7N O 0 1 N N N N N N 59.519 51.083 137.146 -5.560 0.054 -0.356 O7N TXD 1
TXD C7N C7N C 0 1 N N N N N N 58.883 50.245 137.769 -5.514 1.183 0.125 C7N TXD 2
TXD N7N N7N N 0 1 N N N N N N 59.159 49.995 139.047 -6.235 2.253 -0.349 N7N TXD 3
TXD C3N C3N C 0 1 N N R N N N 57.771 49.498 137.074 -4.632 1.517 1.292 C3N TXD 4
TXD C2N C2N C 0 1 N N N N N N 56.756 48.862 137.781 -3.265 2.022 0.828 C2N TXD 5
TXD C4N C4N C 0 1 N N N N N N 57.766 49.445 135.567 -4.576 0.288 2.149 C4N TXD 6
TXD C5N C5N C 0 1 N N N N N N 56.653 48.715 134.998 -3.498 -0.507 2.200 C5N TXD 7
TXD C6N C6N C 0 1 N N N N N N 55.709 48.117 135.808 -2.262 -0.279 1.388 C6N TXD 8
TXD N1N N1N N 0 1 N N N N N N 55.769 48.201 137.143 -2.389 0.876 0.459 N1N TXD 9
TXD "C1'A" C1* C 0 0 N N R N N N 54.718 47.544 137.920 -1.616 0.912 -0.791 "C1'A" TXD 10
TXD "O4'A" O4* O 0 0 N N N N N N 54.602 46.161 137.584 -0.806 -0.244 -1.075 "O4'A" TXD 11
TXD "C2'A" C2* C 0 0 N N R N N N 53.332 48.116 137.663 -0.664 2.101 -0.746 "C2'A" TXD 12
TXD "O2'A" O2* O 0 0 N N N N N N 53.142 49.377 138.301 -1.276 3.314 -1.145 "O2'A" TXD 13
TXD "C3'A" C3* C 0 0 N N S N N N 52.467 47.000 138.206 0.423 1.674 -1.712 "C3'A" TXD 14
TXD "O3'A" O3* O 0 0 N N N N N N 52.244 47.173 139.608 -0.027 1.866 -3.054 "O3'A" TXD 15
TXD "C4'A" C4* C 0 0 N N R N N N 53.284 45.732 137.953 0.524 0.180 -1.439 "C4'A" TXD 16
TXD "C5'A" C5* C 0 0 N N N N N N 52.692 44.815 136.880 1.464 -0.159 -0.290 "C5'A" TXD 17
TXD "O5'A" O5* O 0 0 N N N N N N 52.467 45.503 135.649 1.476 -1.565 -0.115 "O5'A" TXD 18
TXD PN PN P 0 1 N N R N N N 51.928 44.720 134.340 2.405 -2.190 1.054 PN TXD 19
TXD O1N O1N O 0 1 N N N N N N 51.690 45.746 133.264 2.370 -3.684 1.184 O1N TXD 20
TXD O2N O2N O 0 1 N N N N N N 52.815 43.542 134.050 3.868 -1.563 0.765 O2N TXD 21
TXD O3 O3 O 0 1 N N N N N N 50.506 44.123 134.796 1.920 -1.388 2.371 O3 TXD 22
TXD PA PA P 0 1 N N S N N N 49.932 42.761 134.150 2.495 -1.383 3.882 PA TXD 23
TXD O2P O2P O 0 1 N N N N N N 50.261 41.614 135.075 3.972 -0.744 3.714 O2P TXD 24
TXD O1P O1P O 0 1 N N N N N N 50.330 42.672 132.698 2.474 -2.726 4.553 O1P TXD 25
TXD "O5'" "O5'" O 0 1 N N N N N N 48.343 43.002 134.212 1.642 -0.235 4.638 "O5'" TXD 26
TXD "C5'" "C5'" C 0 1 N N N N N N 47.781 44.190 133.661 1.586 1.076 4.100 "C5'" TXD 27
TXD "C4'" "C4'" C 0 1 N N R N N N 46.816 44.834 134.643 0.725 1.943 5.001 "C4'" TXD 28
TXD "C3'" "C3'" C 0 1 N N S N N N 47.373 45.069 136.046 0.605 3.380 4.523 "C3'" TXD 29
TXD "O3'" "O3'" O 0 1 N N N N N N 47.429 46.476 136.299 -0.361 3.522 3.504 "O3'" TXD 30
TXD "C2'" "C2'" C 0 1 N N R N N N 46.399 44.363 136.972 0.248 4.116 5.801 "C2'" TXD 31
TXD "O2'" "O2'" O 0 1 N N N N N N 46.112 45.113 138.150 -1.154 4.057 6.057 "O2'" TXD 32
TXD "C1'" "C1'" C 0 1 N N R N N N 45.160 44.219 136.104 0.990 3.316 6.872 "C1'" TXD 33
TXD "O4'" "O4'" O 0 1 N N N N N N 45.674 43.997 134.799 1.320 2.029 6.307 "O4'" TXD 34
TXD N9A N9A N 0 1 Y N N N N N 44.228 43.135 136.499 2.212 3.966 7.349 N9A TXD 35
TXD C4A C4A C 0 1 Y N N N N N 42.906 43.289 136.579 2.336 4.786 8.436 C4A TXD 36
TXD N3A N3A N 0 1 Y N N N N N 42.081 44.349 136.363 1.370 5.165 9.287 N3A TXD 37
TXD C2A C2A C 0 1 Y N N N N N 40.747 44.239 136.521 1.874 5.981 10.238 C2A TXD 38
TXD N1A N1A N 0 1 Y N N N N N 40.168 43.078 136.886 3.148 6.414 10.400 N1A TXD 39
TXD C6A C6A C 0 1 Y N N N N N 40.910 41.970 137.125 4.070 5.990 9.503 C6A TXD 40
TXD N6A N6A N 0 1 N N N N N N 40.339 40.798 137.499 5.409 6.404 9.616 N6A TXD 41
TXD C5A C5A C 0 1 Y N N N N N 42.380 42.070 136.960 3.674 5.144 8.473 C5A TXD 42
TXD N7A N7A N 0 1 Y N N N N N 43.399 41.203 137.096 4.361 4.562 7.437 N7A TXD 43
TXD C8A C8A C 0 1 Y N N N N N 44.533 41.868 136.806 3.456 3.863 6.783 C8A TXD 44
TXD H7N1 1H7N H 0 0 N N N N N N 58.542 49.288 139.393 -6.855 2.111 -1.140 H7N1 TXD 45
TXD H7N2 2H7N H 0 0 N N N N N N 59.875 50.446 139.580 -6.172 3.180 0.060 H7N2 TXD 46
TXD H2N1 1H2N H 0 0 N N N N N N 56.758 48.898 138.860 -3.347 2.682 -0.043 H2N1 TXD 47
TXD H2N2 2H2N H 0 0 N N N N N N 56.780 48.838 136.682 -2.749 2.558 1.631 H2N2 TXD 48
TXD H6N1 1H6N H 0 0 N N N N N N 54.899 47.566 135.352 -1.407 -0.074 2.038 H6N1 TXD 49
TXD H6N2 2H6N H 0 0 N N N N N N 56.536 48.669 136.279 -2.047 -1.164 0.781 H6N2 TXD 50
TXD H3N H3N H 0 1 N N N N N N 57.637 49.407 138.162 -5.133 2.321 1.842 H3N TXD 51
TXD H4N H4N H 0 1 N N N N N N 58.529 49.913 134.963 -5.444 0.045 2.756 H4N TXD 52
TXD H5N H5N H 0 1 N N N N N N 56.560 48.637 133.925 -3.514 -1.378 2.850 H5N TXD 53
TXD "H1'A" H1* H 0 0 N N N N N N 55.024 47.704 138.964 -2.353 1.015 -1.594 "H1'A" TXD 54
TXD "H2'A" H2* H 0 0 N N N N N N 53.110 48.363 136.614 -0.236 2.239 0.255 "H2'A" TXD 55
TXD HO2A HO2* H 0 0 N N N N N N 53.100 49.253 139.242 -1.139 3.402 -2.104 HO2A TXD 56
TXD "H3'A" H3* H 0 0 N N N N N N 51.476 46.969 137.730 1.361 2.222 -1.593 "H3'A" TXD 57
TXD HO3A HO3* H 0 0 N N N N N N 53.079 47.211 140.060 -0.387 1.015 -3.346 HO3A TXD 58
TXD "H4'A" H4* H 0 0 N N N N N N 53.286 45.121 138.868 0.821 -0.382 -2.330 "H4'A" TXD 59
TXD "H5'1" 1H5* H 0 0 N N N N N N 51.730 44.424 137.244 1.117 0.314 0.630 "H5'1" TXD 60
TXD "H5'2" 2H5* H 0 0 N N N N N N 53.412 44.005 136.690 2.475 0.182 -0.518 "H5'2" TXD 61
TXD HO2N HO2N H 0 0 N N N N N N 53.002 43.507 133.119 4.420 -1.953 0.054 HO2N TXD 62
TXD HO2P HO2P H 0 0 N N N N N N 50.330 40.811 134.572 4.584 -0.759 4.480 HO2P TXD 63
TXD "H5'A" "1H5'" H 0 0 N N N N N N 48.591 44.899 133.436 2.602 1.475 4.040 "H5'A" TXD 64
TXD "H5'B" "2H5'" H 0 0 N N N N N N 47.232 43.930 132.744 1.159 1.026 3.094 "H5'B" TXD 65
TXD "H4'" "H4'" H 0 1 N N N N N N 46.589 45.817 134.205 -0.261 1.474 5.102 "H4'" TXD 66
TXD "H3'" "H3'" H 0 1 N N N N N N 48.394 44.684 136.185 1.572 3.738 4.151 "H3'" TXD 67
TXD "HO3'" "HO3'" H 0 0 N N N N N N 47.441 46.629 137.236 -0.102 4.300 2.987 "HO3'" TXD 68
TXD "H2'" "H2'" H 0 1 N N N N N N 46.798 43.410 137.349 0.521 5.175 5.767 "H2'" TXD 69
TXD "HO2'" "HO2'" H 0 0 N N N N N N 46.048 44.524 138.893 -1.347 3.166 6.400 "HO2'" TXD 70
TXD "H1'" "H1'" H 0 1 N N N N N N 44.536 45.120 136.197 0.384 3.152 7.769 "H1'" TXD 71
TXD H2A H2A H 0 1 N N N N N N 40.125 45.105 136.350 1.162 6.339 10.975 H2A TXD 72
TXD H6A1 1H6A H 0 0 N N N N N N 40.198 40.223 136.693 5.729 7.189 9.081 H6A1 TXD 73
TXD H6A2 2H6A H 0 0 N N N N N N 40.939 40.326 138.144 6.050 5.855 10.157 H6A2 TXD 74
TXD H8A H8A H 0 1 N N N N N N 45.528 41.448 136.819 3.640 3.266 5.899 H8A TXD 75
#
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
TXD O7N C7N DOUB N N 1
TXD C7N C3N SING N N 2
TXD C7N N7N SING N N 3
TXD N7N H7N1 SING N N 4
TXD N7N H7N2 SING N N 5
TXD C3N C4N SING N N 6
TXD C3N C2N SING N N 7
TXD C3N H3N SING N N 8
TXD C2N N1N SING N N 9
TXD C2N H2N1 SING N N 10
TXD C2N H2N2 SING N N 11
TXD C4N C5N DOUB N N 12
TXD C4N H4N SING N N 13
TXD C5N C6N SING N N 14
TXD C5N H5N SING N N 15
TXD C6N N1N SING N N 16
TXD C6N H6N1 SING N N 17
TXD C6N H6N2 SING N N 18
TXD N1N "C1'A" SING N N 19
TXD "C1'A" "O4'A" SING N N 20
TXD "C1'A" "C2'A" SING N N 21
TXD "C1'A" "H1'A" SING N N 22
TXD "O4'A" "C4'A" SING N N 23
TXD "C2'A" "C3'A" SING N N 24
TXD "C2'A" "O2'A" SING N N 25
TXD "C2'A" "H2'A" SING N N 26
TXD "O2'A" HO2A SING N N 27
TXD "C3'A" "C4'A" SING N N 28
TXD "C3'A" "O3'A" SING N N 29
TXD "C3'A" "H3'A" SING N N 30
TXD "O3'A" HO3A SING N N 31
TXD "C4'A" "C5'A" SING N N 32
TXD "C4'A" "H4'A" SING N N 33
TXD "C5'A" "O5'A" SING N N 34
TXD "C5'A" "H5'1" SING N N 35
TXD "C5'A" "H5'2" SING N N 36
TXD "O5'A" PN SING N N 37
TXD PN O1N DOUB N N 38
TXD PN O2N SING N N 39
TXD PN O3 SING N N 40
TXD O2N HO2N SING N N 41
TXD O3 PA SING N N 42
TXD PA O1P DOUB N N 43
TXD PA "O5'" SING N N 44
TXD PA O2P SING N N 45
TXD O2P HO2P SING N N 46
TXD "O5'" "C5'" SING N N 47
TXD "C5'" "C4'" SING N N 48
TXD "C5'" "H5'A" SING N N 49
TXD "C5'" "H5'B" SING N N 50
TXD "C4'" "O4'" SING N N 51
TXD "C4'" "C3'" SING N N 52
TXD "C4'" "H4'" SING N N 53
TXD "C3'" "O3'" SING N N 54
TXD "C3'" "C2'" SING N N 55
TXD "C3'" "H3'" SING N N 56
TXD "O3'" "HO3'" SING N N 57
TXD "C2'" "C1'" SING N N 58
TXD "C2'" "O2'" SING N N 59
TXD "C2'" "H2'" SING N N 60
TXD "O2'" "HO2'" SING N N 61
TXD "C1'" "O4'" SING N N 62
TXD "C1'" N9A SING N N 63
TXD "C1'" "H1'" SING N N 64
TXD N9A C4A SING Y N 65
TXD N9A C8A SING Y N 66
TXD C4A N3A SING Y N 67
TXD C4A C5A DOUB Y N 68
TXD N3A C2A DOUB Y N 69
TXD C2A N1A SING Y N 70
TXD C2A H2A SING N N 71
TXD N1A C6A DOUB Y N 72
TXD C6A C5A SING Y N 73
TXD C6A N6A SING N N 74
TXD N6A H6A1 SING N N 75
TXD N6A H6A2 SING N N 76
TXD C5A N7A SING Y N 77
TXD N7A C8A DOUB Y N 78
TXD C8A H8A SING N N 79
#
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
TXD SMILES_CANONICAL CACTVS 3.341 NC(=O)[C@H]1CN(CC=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
TXD SMILES CACTVS 3.341 NC(=O)[CH]1CN(CC=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
TXD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5CC=CC(C5)C(=O)N)O)O)O)O)N
TXD SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5CC=CC(C5)C(=O)N)O)O)O)O)N
TXD InChI InChI 1.03 InChI=1S/C21H31N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-2,7-11,13-16,20-21,29-32H,3-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t9?,10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
TXD InChIKey InChI 1.03 GFDCQHGWOHYWLP-BFAIWXBASA-N
#
_pdbx_chem_comp_identifier.comp_id TXD
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.5.0
_pdbx_chem_comp_identifier.identifier
"[(2R,3S,4R,5R)-5-(3-aminocarbonyl-3,6-dihydro-2H-pyridin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
TXD 'Create component' 2007-02-15 RCSB
TXD 'Modify descriptor' 2011-06-04 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
TXD O7N O 16.243 5.386 1
TXD C7N C 16.709 6.811 2
TXD N7N N 18.177 7.121 3
TXD C3N C 15.707 7.928 4
TXD C2N C 14.239 7.619 5
TXD C4N C 16.173 9.354 6
TXD C5N C 15.171 10.470 7
TXD C6N C 13.704 10.161 8
TXD N1N N 13.238 8.735 9
TXD "C1'A" C 11.770 8.426 10
TXD "O4'A" O 11.157 7.056 11
TXD "C2'A" C 10.657 9.431 12
TXD "O2'A" O 10.816 10.923 13
TXD "C3'A" C 9.357 8.684 14
TXD "O3'A" O 7.987 9.296 15
TXD "C4'A" C 9.666 7.216 16
TXD "C5'A" C 8.660 6.103 17
TXD "O5'A" O 9.121 4.675 18
TXD PN P 8.116 3.562 19
TXD O1N O 7.003 4.568 20
TXD O2N O 9.229 2.557 21
TXD O3 O 7.110 2.449 22
TXD PA P 7.571 1.022 23
TXD O2P O 6.144 0.561 24
TXD O1P O 8.998 1.483 25
TXD "O5'" O 8.032 -0.405 26
TXD "C5'" C 7.027 -1.518 27
TXD "C4'" C 7.487 -2.946 28
TXD "C3'" C 8.913 -3.412 29
TXD "O3'" O 10.129 -2.532 30
TXD "C2'" C 8.911 -4.912 31
TXD "O2'" O 10.123 -5.796 32
TXD "C1'" C 7.483 -5.373 33
TXD "O4'" O 6.604 -4.158 34
TXD N9A N 7.018 -6.799 35
TXD C4A C 5.598 -7.256 36
TXD N3A N 4.299 -6.506 37
TXD C2A C 3.000 -7.256 38
TXD N1A N 3.000 -8.756 39
TXD C6A C 4.299 -9.506 40
TXD N6A N 4.299 -11.006 41
TXD C5A C 5.598 -8.756 42
TXD N7A N 7.018 -9.213 43
TXD C8A C 7.893 -8.006 44
#
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
TXD O7N C7N DOUBLE NONE 1
TXD C7N C3N SINGLE NONE 2
TXD C7N N7N SINGLE NONE 3
TXD C3N C4N SINGLE NONE 4
TXD C3N C2N SINGLE NONE 5
TXD C2N N1N SINGLE NONE 6
TXD C4N C5N DOUBLE NONE 7
TXD C5N C6N SINGLE NONE 8
TXD C6N N1N SINGLE NONE 9
TXD "C1'A" N1N SINGLE BEGINDASH 10
TXD "C1'A" "O4'A" SINGLE NONE 11
TXD "C1'A" "C2'A" SINGLE NONE 12
TXD "O4'A" "C4'A" SINGLE NONE 13
TXD "C2'A" "C3'A" SINGLE NONE 14
TXD "C2'A" "O2'A" SINGLE BEGINWEDGE 15
TXD "C3'A" "C4'A" SINGLE NONE 16
TXD "C3'A" "O3'A" SINGLE BEGINWEDGE 17
TXD "C4'A" "C5'A" SINGLE BEGINDASH 18
TXD "C5'A" "O5'A" SINGLE NONE 19
TXD "O5'A" PN SINGLE NONE 20
TXD PN O1N DOUBLE NONE 21
TXD PN O2N SINGLE BEGINDASH 22
TXD PN O3 SINGLE NONE 23
TXD O3 PA SINGLE NONE 24
TXD PA O1P DOUBLE NONE 25
TXD PA "O5'" SINGLE NONE 26
TXD PA O2P SINGLE BEGINWEDGE 27
TXD "O5'" "C5'" SINGLE NONE 28
TXD "C4'" "C5'" SINGLE BEGINDASH 29
TXD "C4'" "O4'" SINGLE NONE 30
TXD "C4'" "C3'" SINGLE NONE 31
TXD "C3'" "O3'" SINGLE BEGINWEDGE 32
TXD "C3'" "C2'" SINGLE NONE 33
TXD "C2'" "C1'" SINGLE NONE 34
TXD "C2'" "O2'" SINGLE BEGINWEDGE 35
TXD "C1'" "O4'" SINGLE NONE 36
TXD "C1'" N9A SINGLE BEGINDASH 37
TXD N9A C4A SINGLE NONE 38
TXD N9A C8A SINGLE NONE 39
TXD C4A N3A DOUBLE NONE 40
TXD C4A C5A SINGLE NONE 41
TXD N3A C2A SINGLE NONE 42
TXD C2A N1A DOUBLE NONE 43
TXD N1A C6A SINGLE NONE 44
TXD C6A C5A DOUBLE NONE 45
TXD C6A N6A SINGLE NONE 46
TXD C5A N7A SINGLE NONE 47
TXD N7A C8A DOUBLE NONE 48
#
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
TXD MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CC[C@H](N2CC=CCC2)O1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C20H29N5O7P2/c26-33(28-11-15-4-6-18(30-15)24-8-2-1-3-9-24)32-34(27)29-12-16-5-7-19(31-16)25-14-23-17-10-21-13-22-20(17)25/h1-2,10,13-16,18-19,33-34H,3-9,11-12H2/t15-,16-,18+,19+/m0/s1 KNWGDXXWOLCMQS-RNIPGJKVSA-N
TXD 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
TXD amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
TXD imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
TXD 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
TXD 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
TXD pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
TXD 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
TXD C3N S1 1
TXD C2N S1 1
TXD C4N S1 1
TXD C5N S1 1
TXD C6N S1 1
TXD N1N S1 1
TXD "C1'A" S1 1
TXD "O4'A" S1 1
TXD "C2'A" S1 1
TXD "C3'A" S1 1
TXD "C4'A" S1 1
TXD "C5'A" S1 1
TXD "O5'A" S1 1
TXD PN S1 1
TXD O1N S1 1
TXD O3 S1 1
TXD PA S1 1
TXD O1P S1 1
TXD "O5'" S1 1
TXD "C5'" S1 1
TXD "C4'" S1 1
TXD "C3'" S1 1
TXD "C2'" S1 1
TXD "C1'" S1 1
TXD "O4'" S1 1
TXD N9A S1 1
TXD C4A S1 1
TXD N3A S1 1
TXD C2A S1 1
TXD N1A S1 1
TXD C6A S1 1
TXD C5A S1 1
TXD N7A S1 1
TXD C8A S1 1
TXD N1A F1 1
TXD C6A F1 1
TXD C5A F1 1
TXD C4A F1 1
TXD N3A F1 1
TXD C2A F1 1
TXD N9A F1 1
TXD C8A F1 1
TXD N7A F1 1
TXD N6A F1 1
TXD N7N F2 1
TXD C7N F2 1
TXD O7N F2 1
TXD C3N F2 1
TXD C4A F3 1
TXD C5A F3 1
TXD N7A F3 1
TXD C8A F3 1
TXD N9A F3 1
TXD "O5'A" F4 1
TXD PN F4 1
TXD O1N F4 1
TXD O2N F4 1
TXD O3 F4 1
TXD O3 F4 2
TXD PA F4 2
TXD O1P F4 2
TXD "O5'" F4 2
TXD O2P F4 2
TXD N7A F5 1
TXD C8A F5 1
TXD N9A F5 1
TXD C4A F5 1
TXD C5A F5 1
TXD C6A F5 1
TXD N1A F5 1
TXD C2A F5 1
TXD N3A F5 1
TXD C5A F6 1
TXD C4A F6 1
TXD N3A F6 1
TXD C2A F6 1
TXD N1A F6 1
TXD C6A F6 1
TXD "C2'A" F7 1
TXD "C3'A" F7 1
TXD "C4'A" F7 1
TXD "O4'A" F7 1
TXD "C1'A" F7 1
TXD "C5'A" F7 1
TXD "O5'A" F7 1
TXD "O3'A" F7 1
TXD "O2'A" F7 1
TXD "C2'" F7 2
TXD "C3'" F7 2
TXD "C4'" F7 2
TXD "O4'" F7 2
TXD "C1'" F7 2
TXD "C5'" F7 2
TXD "O5'" F7 2
TXD "O3'" F7 2
TXD "O2'" F7 2
#
_pdbe_chem_comp_rdkit_properties.comp_id TXD
_pdbe_chem_comp_rdkit_properties.exactmw 667.140
_pdbe_chem_comp_rdkit_properties.amw 667.462
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 21
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 20
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 44
_pdbe_chem_comp_rdkit_properties.NumAtoms 75
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 23
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.619
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 5
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 11
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.labuteASA 291.663
_pdbe_chem_comp_rdkit_properties.tpsa 317.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP -4.111
_pdbe_chem_comp_rdkit_properties.CrippenMR 139.341
_pdbe_chem_comp_rdkit_properties.chi0v 22.029
_pdbe_chem_comp_rdkit_properties.chi1v 13.508
_pdbe_chem_comp_rdkit_properties.chi2v 6.949
_pdbe_chem_comp_rdkit_properties.chi3v 6.949
_pdbe_chem_comp_rdkit_properties.chi4v 4.582
_pdbe_chem_comp_rdkit_properties.chi0n 51.240
_pdbe_chem_comp_rdkit_properties.chi1n 25.325
_pdbe_chem_comp_rdkit_properties.chi2n 4.719
_pdbe_chem_comp_rdkit_properties.chi3n 4.719
_pdbe_chem_comp_rdkit_properties.chi4n 2.946
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.460
_pdbe_chem_comp_rdkit_properties.kappa1 11.654
_pdbe_chem_comp_rdkit_properties.kappa2 12.738
_pdbe_chem_comp_rdkit_properties.kappa3 6.858
_pdbe_chem_comp_rdkit_properties.Phi 3.374
#
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
TXD UniChem PDBe TXD
TXD UniChem PubChem 4369002
#
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
TXD O7N 6.845 2.084 -1.508 ETKDGv3 1
TXD C7N 7.300 0.925 -1.704 ETKDGv3 2
TXD N7N 8.330 0.730 -2.674 ETKDGv3 3
TXD C3N 6.734 -0.249 -0.947 ETKDGv3 4
TXD C2N 5.324 -0.595 -1.457 ETKDGv3 5
TXD C4N 6.724 0.049 0.535 ETKDGv3 6
TXD C5N 5.599 0.369 1.194 ETKDGv3 7
TXD C6N 4.243 0.301 0.537 ETKDGv3 8
TXD N1N 4.356 0.389 -0.935 ETKDGv3 9
TXD "C1'A" 3.055 0.355 -1.645 ETKDGv3 10
TXD "O4'A" 2.254 1.438 -1.214 ETKDGv3 11
TXD "C2'A" 2.267 -0.965 -1.468 ETKDGv3 12
TXD "O2'A" 1.933 -1.530 -2.716 ETKDGv3 13
TXD "C3'A" 1.041 -0.538 -0.688 ETKDGv3 14
TXD "O3'A" -0.120 -1.213 -1.094 ETKDGv3 15
TXD "C4'A" 0.949 0.947 -1.006 ETKDGv3 16
TXD "C5'A" 0.256 1.740 0.106 ETKDGv3 17
TXD "O5'A" 1.068 1.759 1.258 ETKDGv3 18
TXD PN 0.176 2.460 2.531 ETKDGv3 19
TXD O1N 1.071 2.628 3.740 ETKDGv3 20
TXD O2N -0.389 3.986 2.061 ETKDGv3 21
TXD O3 -1.161 1.475 2.906 ETKDGv3 22
TXD PA -0.589 0.069 3.683 ETKDGv3 23
TXD O2P -0.349 0.405 5.324 ETKDGv3 24
TXD O1P 0.716 -0.422 3.088 ETKDGv3 25
TXD "O5'" -1.784 -1.140 3.544 ETKDGv3 26
TXD "C5'" -1.712 -1.702 2.252 ETKDGv3 27
TXD "C4'" -3.000 -2.487 1.972 ETKDGv3 28
TXD "C3'" -2.949 -3.198 0.619 ETKDGv3 29
TXD "O3'" -3.659 -4.410 0.704 ETKDGv3 30
TXD "C2'" -3.656 -2.220 -0.282 ETKDGv3 31
TXD "O2'" -4.326 -2.871 -1.331 ETKDGv3 32
TXD "C1'" -4.629 -1.541 0.675 ETKDGv3 33
TXD "O4'" -4.099 -1.597 1.982 ETKDGv3 34
TXD N9A -4.862 -0.150 0.290 ETKDGv3 35
TXD C4A -5.688 0.305 -0.763 ETKDGv3 36
TXD N3A -6.605 -0.352 -1.405 ETKDGv3 37
TXD C2A -7.249 0.317 -2.515 ETKDGv3 38
TXD N1A -6.876 1.524 -2.874 ETKDGv3 39
TXD C6A -5.818 2.221 -2.175 ETKDGv3 40
TXD N6A -5.380 3.508 -2.612 ETKDGv3 41
TXD C5A -5.264 1.604 -1.134 ETKDGv3 42
TXD N7A -4.152 1.975 -0.331 ETKDGv3 43
TXD C8A -3.947 0.954 0.461 ETKDGv3 44
TXD H7N1 8.707 -0.223 -2.872 ETKDGv3 45
TXD H7N2 8.713 1.544 -3.204 ETKDGv3 46
TXD H2N1 5.325 -0.599 -2.570 ETKDGv3 47
TXD H2N2 5.065 -1.623 -1.118 ETKDGv3 48
TXD H6N1 3.642 1.151 0.918 ETKDGv3 49
TXD H6N2 3.755 -0.644 0.853 ETKDGv3 50
TXD H3N 7.386 -1.134 -1.109 ETKDGv3 51
TXD H4N 7.672 0.081 1.065 ETKDGv3 52
TXD H5N 5.653 0.592 2.255 ETKDGv3 53
TXD "H1'A" 3.256 0.520 -2.728 ETKDGv3 54
TXD "H2'A" 2.819 -1.732 -0.889 ETKDGv3 55
TXD HO2A 1.409 -0.861 -3.230 ETKDGv3 56
TXD "H3'A" 1.219 -0.694 0.402 ETKDGv3 57
TXD HO3A -0.039 -2.139 -0.746 ETKDGv3 58
TXD "H4'A" 0.369 1.090 -1.947 ETKDGv3 59
TXD "H5'1" -0.733 1.266 0.304 ETKDGv3 60
TXD "H5'2" 0.093 2.778 -0.260 ETKDGv3 61
TXD HO2N 0.425 4.489 1.807 ETKDGv3 62
TXD HO2P -1.224 0.744 5.641 ETKDGv3 63
TXD "H5'A" -0.845 -2.398 2.204 ETKDGv3 64
TXD "H5'B" -1.598 -0.925 1.461 ETKDGv3 65
TXD "H4'" -3.134 -3.234 2.786 ETKDGv3 66
TXD "H3'" -1.903 -3.384 0.278 ETKDGv3 67
TXD "HO3'" -3.352 -4.976 -0.052 ETKDGv3 68
TXD "H2'" -2.911 -1.491 -0.681 ETKDGv3 69
TXD "HO2'" -4.527 -2.177 -2.011 ETKDGv3 70
TXD "H1'" -5.600 -2.085 0.676 ETKDGv3 71
TXD H2A -8.038 -0.185 -3.058 ETKDGv3 72
TXD H6A1 -5.830 3.958 -3.439 ETKDGv3 73
TXD H6A2 -4.612 4.015 -2.117 ETKDGv3 74
TXD H8A -3.140 0.941 1.179 ETKDGv3 75
#