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 2024-09-27 _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 _chem_comp.pdbx_pcm Y # 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 NDP "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 NDP ARG None "Covalent chemical modification" "Amino-acid side chain" "Any position" O3X NH2 ? ? 2 NDP CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" C4N SG ? ? #