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  ? ? 
# 
