data_NDP
#
_chem_comp.id NDP
_chem_comp.name "NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H30 N7 O17 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 745.421
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NDP
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1DGF
_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
NDP PA AP P 0 1 N N S N N N 14.861 11.692 80.503 -1.275 0.043 -0.038 PA NDP 1
NDP O1A AO1 O 0 1 N N N N N N 14.841 12.028 81.946 -1.710 -1.293 -0.500 O1A NDP 2
NDP O2A AO2 O 0 1 N N N N N N 15.549 10.473 80.008 -2.565 0.915 0.371 O2A NDP 3
NDP O5B AO5* O 0 1 N N N N N N 15.390 12.960 79.658 -0.479 0.787 -1.223 O5B NDP 4
NDP C5B AC5* C 0 1 N N N N N N 15.048 14.291 80.053 -1.385 0.901 -2.322 C5B NDP 5
NDP C4B AC4* C 0 1 N N R N N N 15.898 15.228 79.208 -0.687 1.603 -3.489 C4B NDP 6
NDP O4B AO4* O 0 1 N N N N N N 15.467 16.583 79.405 0.439 0.824 -3.924 O4B NDP 7
NDP C3B AC3* C 0 1 N N R N N N 17.372 15.169 79.595 -1.654 1.723 -4.682 C3B NDP 8
NDP O3B AO3* O 0 1 N N N N N N 18.120 14.349 78.693 -1.863 3.094 -5.029 O3B NDP 9
NDP C2B AC2* C 0 1 N N R N N N 17.842 16.619 79.536 -0.927 0.977 -5.832 C2B NDP 10
NDP O2B AO2* O 0 1 N N N N N N 18.974 16.882 78.682 -1.073 1.680 -7.068 O2B NDP 11
NDP C1B AC1* C 0 1 N N R N N N 16.607 17.414 79.124 0.546 1.001 -5.353 C1B NDP 12
NDP N9A AN9 N 0 1 Y N N N N N 16.449 18.688 79.870 1.304 -0.099 -5.954 N9A NDP 13
NDP C8A AC8 C 0 1 Y N N N N N 16.645 18.917 81.183 1.388 -1.374 -5.479 C8A NDP 14
NDP N7A AN7 N 0 1 Y N N N N N 16.316 20.173 81.516 2.145 -2.090 -6.259 N7A NDP 15
NDP C5A AC5 C 0 1 Y N N N N N 15.904 20.700 80.370 2.594 -1.322 -7.280 C5A NDP 16
NDP C6A AC6 C 0 1 Y N N N N N 15.427 22.002 80.198 3.422 -1.544 -8.394 C6A NDP 17
NDP N6A AN6 N 0 1 N N N N N N 15.438 22.917 81.172 3.976 -2.791 -8.627 N6A NDP 18
NDP N1A AN1 N 0 1 Y N N N N N 15.048 22.316 78.931 3.659 -0.530 -9.219 N1A NDP 19
NDP C2A AC2 C 0 1 Y N N N N N 15.134 21.440 77.919 3.134 0.662 -9.005 C2A NDP 20
NDP N3A AN3 N 0 1 Y N N N N N 15.591 20.197 78.097 2.354 0.916 -7.976 N3A NDP 21
NDP C4A AC4 C 0 1 Y N N N N N 15.981 19.802 79.324 2.056 -0.037 -7.100 C4A NDP 22
NDP O3 O3 O 0 1 N N N N N N 13.327 11.628 80.057 -0.309 -0.118 1.238 O3 NDP 23
NDP PN NP P 0 1 N N S N N N 12.528 11.132 78.764 -1.165 -0.865 2.378 PN NDP 24
NDP O1N NO1 O 0 1 N N N N N N 13.486 10.811 77.681 -2.352 -0.049 2.718 O1N NDP 25
NDP O2N NO2 O 0 1 N N N N N N 11.586 10.083 79.201 -1.640 -2.304 1.835 O2N NDP 26
NDP O5D NO5* O 0 1 N N N N N N 11.722 12.466 78.364 -0.255 -1.061 3.692 O5D NDP 27
NDP C5D NC5* C 0 1 N N N N N N 10.803 13.113 79.263 -1.066 -1.726 4.661 C5D NDP 28
NDP C4D NC4* C 0 1 N N R N N N 10.675 14.572 78.840 -0.257 -1.944 5.941 C4D NDP 29
NDP O4D NO4* O 0 1 N N N N N N 11.988 15.188 78.828 0.150 -0.676 6.500 O4D NDP 30
NDP C3D NC3* C 0 1 N N S N N N 10.133 14.710 77.427 -1.136 -2.592 7.033 C3D NDP 31
NDP O3D NO3* O 0 1 N N N N N N 8.701 14.684 77.373 -0.916 -4.003 7.081 O3D NDP 32
NDP C2D NC2* C 0 1 N N R N N N 10.734 16.055 77.007 -0.661 -1.924 8.345 C2D NDP 33
NDP O2D NO2* O 0 1 N N N N N N 9.893 17.147 77.361 -0.136 -2.903 9.244 O2D NDP 34
NDP C1D NC1* C 0 1 N N R N N N 12.058 16.172 77.760 0.446 -0.949 7.887 C1D NDP 35
NDP N1N NN1 N 0 1 N N N N N N 13.254 15.953 76.900 0.394 0.286 8.672 N1N NDP 36
NDP C2N NC2 C 0 1 N N N N N N 13.460 14.684 76.332 1.485 0.682 9.394 C2N NDP 37
NDP C3N NC3 C 0 1 N N N N N N 14.497 14.477 75.434 1.592 1.952 9.826 C3N NDP 38
NDP C7N NC7 C 0 1 N N N N N N 14.570 13.149 74.676 2.727 2.334 10.580 C7N NDP 39
NDP O7N NO7 O 0 1 N N N N N N 15.195 13.084 73.617 3.594 1.517 10.831 O7N NDP 40
NDP N7N NN7 N 0 1 N N N N N N 13.875 12.134 75.201 2.848 3.602 11.019 N7N NDP 41
NDP C4N NC4 C 0 1 N N N N N N 15.372 15.535 75.135 0.528 2.970 9.530 C4N NDP 42
NDP C5N NC5 C 0 1 N N N N N N 15.197 16.797 75.724 -0.737 2.307 9.075 C5N NDP 43
NDP C6N NC6 C 0 1 N N N N N N 14.129 17.013 76.594 -0.762 1.053 8.683 C6N NDP 44
NDP P2B AP2* P 0 1 N N N N N N 20.498 16.705 79.233 -1.639 0.622 -8.141 P2B NDP 45
NDP O1X AOP1 O 0 1 N N N N N N 20.729 15.259 78.980 -2.944 0.099 -7.677 O1X NDP 46
NDP O2X AOP2 O 0 1 N N N N N N 20.487 17.102 80.666 -1.829 1.351 -9.564 O2X NDP 47
NDP O3X AOP3 O 0 1 N N N N N N 21.297 17.612 78.377 -0.597 -0.594 -8.296 O3X NDP 48
NDP HOA2 2HOA H 0 0 N N N N N N 15.561 10.257 79.082 -2.238 1.777 0.665 HOA2 NDP 49
NDP H51A AH51 H 0 0 N N N N N N 13.955 14.504 79.983 -1.703 -0.093 -2.635 H51A NDP 50
NDP H52A AH52 H 0 0 N N N N N N 15.155 14.466 81.148 -2.256 1.481 -2.017 H52A NDP 51
NDP H4B AH4* H 0 1 N N N N N N 15.777 14.903 78.148 -0.355 2.594 -3.179 H4B NDP 52
NDP H3B AH3* H 0 1 N N N N N N 17.519 14.715 80.602 -2.604 1.239 -4.454 H3B NDP 53
NDP HO3A AHO3 H 0 0 N N N N N N 19.038 14.312 78.934 -2.317 3.505 -4.281 HO3A NDP 54
NDP H2B AH2* H 0 1 N N N N N N 18.244 16.917 80.532 -1.290 -0.046 -5.924 H2B NDP 55
NDP H1B AH1* H 0 1 N N N N N N 16.706 17.682 78.046 1.011 1.958 -5.588 H1B NDP 56
NDP H8A AH8 H 0 1 N N N N N N 17.027 18.168 81.897 0.898 -1.737 -4.588 H8A NDP 57
NDP H61A AH61 H 0 0 N N N N N N 15.089 23.867 81.046 4.545 -2.932 -9.399 H61A NDP 58
NDP H62A AH62 H 0 0 N N N N N N 16.396 22.986 81.514 3.795 -3.524 -8.018 H62A NDP 59
NDP H2A AH2 H 0 1 N N N N N N 14.819 21.751 76.908 3.354 1.459 -9.700 H2A NDP 60
NDP H21N NH21 H 0 0 N N N N N N 11.111 9.788 78.433 -0.838 -2.803 1.626 H21N NDP 61
NDP H51N NH51 H 0 0 N N N N N N 9.818 12.593 79.320 -1.388 -2.690 4.267 H51N NDP 62
NDP H52N NH52 H 0 0 N N N N N N 11.094 12.998 80.333 -1.941 -1.115 4.884 H52N NDP 63
NDP H4D NH4* H 0 1 N N N N N N 9.980 15.056 79.565 0.614 -2.566 5.737 H4D NDP 64
NDP H3D NH3* H 0 1 N N N N N N 10.407 13.867 76.750 -2.189 -2.377 6.853 H3D NDP 65
NDP HO3N NHO3 H 0 0 N N N N N N 8.362 14.770 76.489 -1.489 -4.352 7.777 HO3N NDP 66
NDP H2D NH2* H 0 1 N N N N N N 10.861 16.092 75.899 -1.480 -1.377 8.813 H2D NDP 67
NDP HO2N NHO2 H 0 0 N N N N N N 10.265 17.981 77.100 -0.857 -3.514 9.444 HO2N NDP 68
NDP H1D NH1* H 0 1 N N N N N N 12.186 17.209 78.147 1.426 -1.417 7.981 H1D NDP 69
NDP H2N NH2 H 0 1 N N N N N N 12.799 13.840 76.594 2.266 -0.028 9.619 H2N NDP 70
NDP H71N NH71 H 0 0 N N N N N N 13.357 12.187 76.078 3.626 3.864 11.535 H71N NDP 71
NDP H72N NH72 H 0 0 N N N N N N 13.923 11.249 74.695 2.159 4.254 10.815 H72N NDP 72
NDP H41N NH41 H 0 0 N N N N N N 16.413 15.195 75.342 0.325 3.556 10.426 H41N NDP 73
NDP H42N NH42 H 0 0 N N N N N N 15.393 15.667 74.028 0.888 3.634 8.743 H42N NDP 74
NDP H5N NH5 H 0 1 N N N N N N 15.898 17.618 75.503 -1.656 2.876 9.075 H5N NDP 75
NDP H6N NH6 H 0 1 N N N N N N 13.977 18.012 77.035 -1.695 0.614 8.363 H6N NDP 76
NDP HOP2 2HOP H 0 0 N N N N N N 21.375 16.998 80.987 -2.169 0.684 -10.176 HOP2 NDP 77
NDP HOP3 3HOP H 0 0 N N N N N N 22.185 17.508 78.698 0.236 -0.211 -8.599 HOP3 NDP 78
#
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
NDP PA O1A DOUB N N 1
NDP PA O2A SING N N 2
NDP PA O5B SING N N 3
NDP PA O3 SING N N 4
NDP O2A HOA2 SING N N 5
NDP O5B C5B SING N N 6
NDP C5B C4B SING N N 7
NDP C5B H51A SING N N 8
NDP C5B H52A SING N N 9
NDP C4B O4B SING N N 10
NDP C4B C3B SING N N 11
NDP C4B H4B SING N N 12
NDP O4B C1B SING N N 13
NDP C3B O3B SING N N 14
NDP C3B C2B SING N N 15
NDP C3B H3B SING N N 16
NDP O3B HO3A SING N N 17
NDP C2B O2B SING N N 18
NDP C2B C1B SING N N 19
NDP C2B H2B SING N N 20
NDP O2B P2B SING N N 21
NDP C1B N9A SING N N 22
NDP C1B H1B SING N N 23
NDP N9A C8A SING Y N 24
NDP N9A C4A SING Y N 25
NDP C8A N7A DOUB Y N 26
NDP C8A H8A SING N N 27
NDP N7A C5A SING Y N 28
NDP C5A C6A SING Y N 29
NDP C5A C4A DOUB Y N 30
NDP C6A N6A SING N N 31
NDP C6A N1A DOUB Y N 32
NDP N6A H61A SING N N 33
NDP N6A H62A SING N N 34
NDP N1A C2A SING Y N 35
NDP C2A N3A DOUB Y N 36
NDP C2A H2A SING N N 37
NDP N3A C4A SING Y N 38
NDP O3 PN SING N N 39
NDP PN O1N DOUB N N 40
NDP PN O2N SING N N 41
NDP PN O5D SING N N 42
NDP O2N H21N SING N N 43
NDP O5D C5D SING N N 44
NDP C5D C4D SING N N 45
NDP C5D H51N SING N N 46
NDP C5D H52N SING N N 47
NDP C4D O4D SING N N 48
NDP C4D C3D SING N N 49
NDP C4D H4D SING N N 50
NDP O4D C1D SING N N 51
NDP C3D O3D SING N N 52
NDP C3D C2D SING N N 53
NDP C3D H3D SING N N 54
NDP O3D HO3N SING N N 55
NDP C2D O2D SING N N 56
NDP C2D C1D SING N N 57
NDP C2D H2D SING N N 58
NDP O2D HO2N SING N N 59
NDP C1D N1N SING N N 60
NDP C1D H1D SING N N 61
NDP N1N C2N SING N N 62
NDP N1N C6N SING N N 63
NDP C2N C3N DOUB N N 64
NDP C2N H2N SING N N 65
NDP C3N C7N SING N N 66
NDP C3N C4N SING N N 67
NDP C7N O7N DOUB N N 68
NDP C7N N7N SING N N 69
NDP N7N H71N SING N N 70
NDP N7N H72N SING N N 71
NDP C4N C5N SING N N 72
NDP C4N H41N SING N N 73
NDP C4N H42N SING N N 74
NDP C5N C6N DOUB N N 75
NDP C5N H5N SING N N 76
NDP C6N H6N SING N N 77
NDP P2B O1X DOUB N N 78
NDP P2B O2X SING N N 79
NDP P2B O3X SING N N 80
NDP O2X HOP2 SING N N 81
NDP O3X HOP3 SING N N 82
#
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
NDP SMILES_CANONICAL CACTVS 3.341 NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
NDP SMILES CACTVS 3.341 NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
NDP 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)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
NDP 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)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
NDP InChI InChI 1.03 InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
NDP InChIKey InChI 1.03 ACFIXJIJDZMPPO-NNYOXOHSSA-N
#
_pdbx_chem_comp_identifier.comp_id NDP
_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-4H-pyridin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-4-phosphonooxy-oxolan-2-yl]methyl 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
NDP 'Create component' 1999-07-08 RCSB
NDP 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id NDP
_pdbe_chem_comp_drugbank_details.drugbank_id DB02338
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name NADPH
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 53-57-6
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
NDP 'Dihydronicotinamide-adenine dinucleotide phosphate' DrugBank ?
NDP 'Reduced nicotinamide adenine dinucleotide phosphate' DrugBank ?
NDP TPNH DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id NDP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02338
_pdbe_chem_comp_drugbank_classification.parent "(5'->5')-dinucleotides"
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class "(5'->5')-dinucleotides"
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
"This compound belongs to the class of organic compounds known as (5'->5')-dinucleotides. These are dinucleotides where the two bases are connected via a (5'->5')-phosphodiester linkage."
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
NDP DB02338 'Thioredoxin reductase 1, cytoplasmic' Humans Q16881 unknown 1
NDP DB02338 'Glucose-6-phosphate 1-dehydrogenase' 'Leuconostoc mesenteroides' P11411 unknown 2
NDP DB02338 'Pteridine reductase 1' 'Leishmania major' Q01782 unknown 3
NDP DB02338 'Glucose--fructose oxidoreductase' 'Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)' Q07982 unknown 4
NDP DB02338 'Dihydropyrimidine dehydrogenase [NADP(+)]' Humans Q12882 unknown 5
NDP DB02338 'Alpha-aminoadipic semialdehyde synthase, mitochondrial' Humans Q9UDR5 unknown 6
#
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
NDP PA P 13.893 -0.203 1
NDP O1A O 12.466 -0.664 2
NDP O2A O 15.320 0.258 3
NDP O5B O 14.354 -1.630 4
NDP C5B C 15.821 -1.945 5
NDP C4B C 16.282 -3.372 6
NDP O4B O 15.398 -4.584 7
NDP C3B C 17.708 -3.838 8
NDP O3B O 18.923 -2.959 9
NDP C2B C 17.705 -5.338 10
NDP O2B O 18.917 -6.222 11
NDP C1B C 16.278 -5.799 12
NDP N9A N 15.812 -7.225 13
NDP C8A C 16.687 -8.432 14
NDP N7A N 15.812 -9.639 15
NDP C5A C 14.393 -9.182 16
NDP C6A C 13.094 -9.932 17
NDP N6A N 13.094 -11.432 18
NDP N1A N 11.794 -9.182 19
NDP C2A C 11.794 -7.682 20
NDP N3A N 13.094 -6.932 21
NDP C4A C 14.393 -7.682 22
NDP O3 O 13.432 1.224 23
NDP PN P 11.966 1.539 24
NDP O1N O 12.280 3.006 25
NDP O2N O 11.651 0.072 26
NDP O5D O 10.499 1.853 27
NDP C5D C 10.038 3.281 28
NDP C4D C 8.571 3.595 29
NDP O4D O 7.963 4.966 30
NDP C3D C 7.455 2.593 31
NDP O3D O 7.609 1.101 32
NDP C2D C 6.157 3.345 33
NDP O2D O 4.785 2.738 34
NDP C1D C 6.471 4.812 35
NDP N1N N 5.470 5.929 36
NDP C2N C 5.936 7.354 37
NDP C3N C 4.934 8.471 38
NDP C7N C 5.400 9.897 39
NDP O7N O 6.867 10.206 40
NDP N7N N 4.398 11.013 41
NDP C4N C 3.466 8.162 42
NDP C5N C 3.000 6.736 43
NDP C6N C 4.002 5.619 44
NDP P2B P 20.289 -5.614 45
NDP O1X O 21.660 -5.006 46
NDP O2X O 20.896 -6.986 47
NDP O3X O 19.681 -4.243 48
#
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
NDP PA O1A DOUBLE NONE 1
NDP PA O2A SINGLE BEGINDASH 2
NDP PA O5B SINGLE NONE 3
NDP PA O3 SINGLE NONE 4
NDP O5B C5B SINGLE NONE 5
NDP C4B C5B SINGLE BEGINDASH 6
NDP C4B O4B SINGLE NONE 7
NDP C4B C3B SINGLE NONE 8
NDP O4B C1B SINGLE NONE 9
NDP C3B O3B SINGLE BEGINWEDGE 10
NDP C3B C2B SINGLE NONE 11
NDP C2B O2B SINGLE BEGINWEDGE 12
NDP C2B C1B SINGLE NONE 13
NDP O2B P2B SINGLE NONE 14
NDP C1B N9A SINGLE BEGINDASH 15
NDP N9A C8A SINGLE NONE 16
NDP N9A C4A SINGLE NONE 17
NDP C8A N7A DOUBLE NONE 18
NDP N7A C5A SINGLE NONE 19
NDP C5A C6A SINGLE NONE 20
NDP C5A C4A DOUBLE NONE 21
NDP C6A N6A SINGLE NONE 22
NDP C6A N1A DOUBLE NONE 23
NDP N1A C2A SINGLE NONE 24
NDP C2A N3A DOUBLE NONE 25
NDP N3A C4A SINGLE NONE 26
NDP O3 PN SINGLE NONE 27
NDP PN O1N DOUBLE NONE 28
NDP PN O2N SINGLE BEGINDASH 29
NDP PN O5D SINGLE NONE 30
NDP O5D C5D SINGLE NONE 31
NDP C4D C5D SINGLE BEGINDASH 32
NDP C4D O4D SINGLE NONE 33
NDP C4D C3D SINGLE NONE 34
NDP O4D C1D SINGLE NONE 35
NDP C3D O3D SINGLE BEGINWEDGE 36
NDP C3D C2D SINGLE NONE 37
NDP C2D O2D SINGLE BEGINWEDGE 38
NDP C2D C1D SINGLE NONE 39
NDP C1D N1N SINGLE BEGINDASH 40
NDP N1N C2N SINGLE NONE 41
NDP N1N C6N SINGLE NONE 42
NDP C2N C3N DOUBLE NONE 43
NDP C3N C7N SINGLE NONE 44
NDP C3N C4N SINGLE NONE 45
NDP C7N O7N DOUBLE NONE 46
NDP C7N N7N SINGLE NONE 47
NDP C4N C5N SINGLE NONE 48
NDP C5N C6N DOUBLE NONE 49
NDP P2B O1X DOUBLE NONE 50
NDP P2B O2X SINGLE NONE 51
NDP P2B O3X SINGLE NONE 52
#
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
NDP MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CC[C@H](N2C=CCC=C2)O1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C20H27N5O7P2/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/h2-3,8-10,13-16,18-19,33-34H,1,4-7,11-12H2/t15-,16-,18+,19+/m0/s1 QMVHHVSTFIPFPP-RNIPGJKVSA-N
NDP 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
NDP amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
NDP imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
NDP 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
NDP 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
NDP pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
NDP 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
NDP PA S1 1
NDP O1A S1 1
NDP O5B S1 1
NDP C5B S1 1
NDP C4B S1 1
NDP O4B S1 1
NDP C3B S1 1
NDP C2B S1 1
NDP C1B S1 1
NDP N9A S1 1
NDP C8A S1 1
NDP N7A S1 1
NDP C5A S1 1
NDP C6A S1 1
NDP N1A S1 1
NDP C2A S1 1
NDP N3A S1 1
NDP C4A S1 1
NDP O3 S1 1
NDP PN S1 1
NDP O1N S1 1
NDP O5D S1 1
NDP C5D S1 1
NDP C4D S1 1
NDP O4D S1 1
NDP C3D S1 1
NDP C2D S1 1
NDP C1D S1 1
NDP N1N S1 1
NDP C2N S1 1
NDP C3N S1 1
NDP C4N S1 1
NDP C5N S1 1
NDP C6N S1 1
NDP N1A F1 1
NDP C6A F1 1
NDP C5A F1 1
NDP C4A F1 1
NDP N3A F1 1
NDP C2A F1 1
NDP N9A F1 1
NDP C8A F1 1
NDP N7A F1 1
NDP N6A F1 1
NDP N7N F2 1
NDP C7N F2 1
NDP O7N F2 1
NDP C3N F2 1
NDP C5A F3 1
NDP C4A F3 1
NDP N9A F3 1
NDP C8A F3 1
NDP N7A F3 1
NDP O2A F4 1
NDP PA F4 1
NDP O1A F4 1
NDP O5B F4 1
NDP O3 F4 1
NDP O2B F4 2
NDP P2B F4 2
NDP O1X F4 2
NDP O2X F4 2
NDP O3X F4 2
NDP O3 F4 3
NDP PN F4 3
NDP O1N F4 3
NDP O2N F4 3
NDP O5D F4 3
NDP N7A F5 1
NDP C8A F5 1
NDP N9A F5 1
NDP C4A F5 1
NDP C5A F5 1
NDP C6A F5 1
NDP N1A F5 1
NDP C2A F5 1
NDP N3A F5 1
NDP C5A F6 1
NDP C6A F6 1
NDP N1A F6 1
NDP C2A F6 1
NDP N3A F6 1
NDP C4A F6 1
NDP C2B F7 1
NDP C3B F7 1
NDP C4B F7 1
NDP O4B F7 1
NDP C1B F7 1
NDP C5B F7 1
NDP O5B F7 1
NDP O3B F7 1
NDP O2B F7 1
NDP C2D F7 2
NDP C3D F7 2
NDP C4D F7 2
NDP O4D F7 2
NDP C1D F7 2
NDP C5D F7 2
NDP O5D F7 2
NDP O3D F7 2
NDP O2D F7 2
#
_pdbe_chem_comp_rdkit_properties.comp_id NDP
_pdbe_chem_comp_rdkit_properties.exactmw 745.091
_pdbe_chem_comp_rdkit_properties.amw 745.425
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 24
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 11
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 21
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 23
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 48
_pdbe_chem_comp_rdkit_properties.NumAtoms 78
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 27
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.524
_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 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 311.112
_pdbe_chem_comp_rdkit_properties.tpsa 364.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.378
_pdbe_chem_comp_rdkit_properties.CrippenMR 149.727
_pdbe_chem_comp_rdkit_properties.chi0v 24.596
_pdbe_chem_comp_rdkit_properties.chi1v 15.699
_pdbe_chem_comp_rdkit_properties.chi2v 7.558
_pdbe_chem_comp_rdkit_properties.chi3v 7.558
_pdbe_chem_comp_rdkit_properties.chi4v 5.159
_pdbe_chem_comp_rdkit_properties.chi0n 51.912
_pdbe_chem_comp_rdkit_properties.chi1n 25.463
_pdbe_chem_comp_rdkit_properties.chi2n 4.922
_pdbe_chem_comp_rdkit_properties.chi3n 4.922
_pdbe_chem_comp_rdkit_properties.chi4n 3.138
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.730
_pdbe_chem_comp_rdkit_properties.kappa1 14.119
_pdbe_chem_comp_rdkit_properties.kappa2 13.882
_pdbe_chem_comp_rdkit_properties.kappa3 8.171
_pdbe_chem_comp_rdkit_properties.Phi 4.083
#
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
NDP UniChem ChEMBL CHEMBL407009
NDP UniChem DrugBank DB02338
NDP UniChem PDBe NDP
NDP UniChem 'KEGG LIGAND' C00005
NDP UniChem ChEBI 16474
NDP UniChem ZINC ZINC000008215411
NDP UniChem fdasrs 381Q4X082D
NDP UniChem SureChEMBL SCHEMBL2041
NDP UniChem HMDB HMDB0000221
NDP UniChem 'PubChem TPHARMA' 14888917
NDP UniChem NMRShiftDB 60020814
NDP UniChem MetaboLights MTBLC16474
NDP UniChem BRENDA 107956
NDP UniChem BRENDA 183396
NDP UniChem BRENDA 40
NDP UniChem BRENDA 5
NDP UniChem BRENDA 6732
NDP UniChem MedChemExpress HY-113325
NDP UniChem 'Probes And Drugs' PD060084
NDP UniChem Nikkaji J213.537J
NDP UniChem PubChem 134821689
NDP UniChem PubChem 5884
NDP UniChem ACTor 22046-90-8
#
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
NDP PA 1.023 0.677 2.248 ETKDGv3 1
NDP O1A 0.285 1.113 3.493 ETKDGv3 2
NDP O2A 1.113 -1.016 2.226 ETKDGv3 3
NDP O5B 2.606 1.309 2.321 ETKDGv3 4
NDP C5B 3.107 1.429 1.010 ETKDGv3 5
NDP C4B 4.611 1.710 1.071 ETKDGv3 6
NDP O4B 5.261 0.644 1.718 ETKDGv3 7
NDP C3B 5.215 1.866 -0.320 ETKDGv3 8
NDP O3B 5.198 3.207 -0.741 ETKDGv3 9
NDP C2B 6.628 1.351 -0.147 ETKDGv3 10
NDP O2B 7.521 2.433 0.044 ETKDGv3 11
NDP C1B 6.537 0.505 1.133 ETKDGv3 12
NDP N9A 6.786 -0.906 0.844 ETKDGv3 13
NDP C8A 7.520 -1.813 1.679 ETKDGv3 14
NDP N7A 7.193 -3.062 1.516 ETKDGv3 15
NDP C5A 6.171 -3.029 0.526 ETKDGv3 16
NDP C6A 5.267 -4.106 0.106 ETKDGv3 17
NDP N6A 5.488 -5.459 0.501 ETKDGv3 18
NDP N1A 4.238 -3.792 -0.637 ETKDGv3 19
NDP C2A 3.985 -2.420 -1.027 ETKDGv3 20
NDP N3A 4.785 -1.462 -0.640 ETKDGv3 21
NDP C4A 5.929 -1.800 0.154 ETKDGv3 22
NDP O3 0.213 1.277 0.871 ETKDGv3 23
NDP PN -1.206 0.361 0.655 ETKDGv3 24
NDP O1N -0.846 -1.022 0.158 ETKDGv3 25
NDP O2N -2.068 0.237 2.109 ETKDGv3 26
NDP O5D -2.167 1.151 -0.511 ETKDGv3 27
NDP C5D -3.350 0.407 -0.694 ETKDGv3 28
NDP C4D -4.259 1.130 -1.696 ETKDGv3 29
NDP O4D -5.358 0.293 -2.005 ETKDGv3 30
NDP C3D -4.777 2.469 -1.139 ETKDGv3 31
NDP O3D -4.724 3.486 -2.114 ETKDGv3 32
NDP C2D -6.193 2.131 -0.734 ETKDGv3 33
NDP O2D -7.079 3.223 -0.815 ETKDGv3 34
NDP C1D -6.546 0.981 -1.674 ETKDGv3 35
NDP N1N -7.511 0.070 -1.043 ETKDGv3 36
NDP C2N -7.070 -0.914 -0.090 ETKDGv3 37
NDP C3N -7.945 -1.717 0.540 ETKDGv3 38
NDP C7N -7.481 -2.740 1.511 ETKDGv3 39
NDP O7N -8.282 -3.170 2.384 ETKDGv3 40
NDP N7N -6.155 -3.276 1.467 ETKDGv3 41
NDP C4N -9.436 -1.564 0.319 ETKDGv3 42
NDP C5N -9.817 -0.526 -0.700 ETKDGv3 43
NDP C6N -8.911 0.234 -1.312 ETKDGv3 44
NDP P2B 9.091 1.986 -0.462 ETKDGv3 45
NDP O1X 9.520 0.696 0.205 ETKDGv3 46
NDP O2X 9.124 1.804 -2.146 ETKDGv3 47
NDP O3X 10.172 3.213 -0.029 ETKDGv3 48
NDP HOA2 1.665 -1.236 1.434 ETKDGv3 49
NDP H51A 2.605 2.278 0.494 ETKDGv3 50
NDP H52A 2.952 0.494 0.424 ETKDGv3 51
NDP H4B 4.782 2.639 1.663 ETKDGv3 52
NDP H3B 4.686 1.224 -1.064 ETKDGv3 53
NDP HO3A 4.268 3.401 -1.028 ETKDGv3 54
NDP H2B 6.878 0.734 -1.044 ETKDGv3 55
NDP H1B 7.293 0.858 1.870 ETKDGv3 56
NDP H8A 8.259 -1.494 2.402 ETKDGv3 57
NDP H61A 4.832 -6.213 0.198 ETKDGv3 58
NDP H62A 6.309 -5.713 1.094 ETKDGv3 59
NDP H2A 3.118 -2.184 -1.630 ETKDGv3 60
NDP H21N -2.362 1.162 2.307 ETKDGv3 61
NDP H51N -3.112 -0.599 -1.108 ETKDGv3 62
NDP H52N -3.903 0.287 0.265 ETKDGv3 63
NDP H4D -3.673 1.301 -2.627 ETKDGv3 64
NDP H3D -4.199 2.811 -0.251 ETKDGv3 65
NDP HO3N -5.168 3.153 -2.937 ETKDGv3 66
NDP H2D -6.180 1.765 0.317 ETKDGv3 67
NDP HO2N -7.230 3.443 -1.770 ETKDGv3 68
NDP H1D -6.969 1.374 -2.626 ETKDGv3 69
NDP H2N -6.015 -0.985 0.132 ETKDGv3 70
NDP H71N -5.842 -3.948 2.203 ETKDGv3 71
NDP H72N -5.512 -3.094 0.666 ETKDGv3 72
NDP H41N -9.852 -2.541 -0.006 ETKDGv3 73
NDP H42N -9.915 -1.290 1.283 ETKDGv3 74
NDP H5N -10.866 -0.380 -0.923 ETKDGv3 75
NDP H6N -9.245 0.982 -2.021 ETKDGv3 76
NDP HOP2 8.944 0.843 -2.310 ETKDGv3 77
NDP HOP3 10.042 3.331 0.946 ETKDGv3 78
#