data_NGD # _chem_comp.id NGD _chem_comp.name ;3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYD ROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- YL]PYRIDINIUM ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H28 N7 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "NICOTINAMIDE GUANINE DINUCLEOTIDE" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2006-12-12 _chem_comp.pdbx_modified_date 2020-06-17 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 680.432 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NGD _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 2O3U _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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.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 NGD O6A O6A O 0 1 N N N 11.546 -0.150 0.691 2.717 -6.099 -4.059 O6A NGD 1 NGD C6A C6A C 0 1 N N N 10.760 0.237 1.589 2.635 -5.837 -2.866 C6A NGD 2 NGD C5A C5A C 0 1 Y N N 10.076 -0.675 2.392 1.730 -4.862 -2.323 C5A NGD 3 NGD N7A N7A N 0 1 Y N N 10.042 -2.015 2.452 0.831 -4.074 -2.980 N7A NGD 4 NGD C8A C8A C 0 1 Y N N 9.195 -2.369 3.433 0.264 -3.371 -2.019 C8A NGD 5 NGD N9A N9A N 0 1 Y N N 8.689 -1.254 3.999 0.766 -3.679 -0.777 N9A NGD 6 NGD C4A C4A C 0 1 Y N N 9.222 -0.195 3.378 1.715 -4.642 -0.966 C4A NGD 7 NGD N3A N3A N 0 1 N N N 9.068 1.144 3.545 2.457 -5.228 -0.001 N3A NGD 8 NGD C2A C2A C 0 1 N N N 9.730 2.017 2.763 3.295 -6.126 -0.470 C2A NGD 9 NGD N2A N2A N 0 1 N N N 9.558 3.354 2.956 4.138 -6.833 0.349 N2A NGD 10 NGD N1A N1A N 0 1 N N N 10.566 1.562 1.793 3.394 -6.432 -1.848 N1A NGD 11 NGD "C1'" C1* C 0 1 N N R 7.704 -1.244 5.121 0.353 -3.080 0.490 "C1'" NGD 12 NGD "O4'" O4* O 0 1 N N N 6.386 -0.797 4.755 -1.048 -2.748 0.436 "O4'" NGD 13 NGD "C2'" C2* C 0 1 N N R 8.083 -0.284 6.232 1.081 -1.790 0.833 "C2'" NGD 14 NGD "O2'" O2* O 0 1 N N N 9.180 -0.785 7.003 2.324 -2.037 1.459 "O2'" NGD 15 NGD "C3'" C3* C 0 1 N N S 6.788 -0.236 7.008 0.080 -1.112 1.748 "C3'" NGD 16 NGD "O3'" O3* O 0 1 N N N 6.789 -1.326 7.920 0.141 -1.707 3.044 "O3'" NGD 17 NGD "C4'" C4* C 0 1 N N R 5.691 -0.511 5.981 -1.252 -1.479 1.101 "C4'" NGD 18 NGD "C5'" C5* C 0 1 N N N 4.571 0.573 5.943 -1.708 -0.462 0.064 "C5'" NGD 19 NGD "O5'" O5* O 0 1 N N N 4.917 1.877 5.463 -1.870 0.797 0.693 "O5'" NGD 20 NGD PA PA P 0 1 N N S 4.705 3.294 6.253 -2.352 2.077 -0.172 PA NGD 21 NGD O1A O1A O 0 1 N N N 3.714 3.287 7.364 -3.717 1.589 -0.889 O1A NGD 22 NGD O2A O2A O 0 1 N N N 6.104 3.830 6.471 -2.485 3.351 0.612 O2A NGD 23 NGD O3 O3 O 0 1 N N N 3.985 4.189 5.110 -1.299 2.159 -1.396 O3 NGD 24 NGD PB PB P 0 1 N N S 4.495 4.302 3.572 0.285 2.478 -1.414 PB NGD 25 NGD O1B O1B O 0 1 N N N 4.069 5.691 3.147 0.669 3.823 -0.868 O1B NGD 26 NGD O2B O2B O 0 1 N N N 5.931 3.853 3.463 0.931 1.216 -0.636 O2B NGD 27 NGD "O5'R" RO5* O 0 0 N N N 3.561 3.252 2.780 0.640 2.214 -2.970 "O5'R" NGD 28 NGD "C5'R" RC5* C 0 0 N N N 2.134 3.370 2.876 0.300 0.961 -3.537 "C5'R" NGD 29 NGD "C4'R" RC4* C 0 0 N N R 1.483 3.786 1.554 0.727 0.945 -4.998 "C4'R" NGD 30 NGD "C3'R" RC3* C 0 0 N N S -0.005 3.508 1.604 0.412 -0.374 -5.696 "C3'R" NGD 31 NGD "O3'R" RO3* O 0 0 N N N -0.752 4.359 0.694 0.271 -0.131 -7.096 "O3'R" NGD 32 NGD "C2'R" RC2* C 0 0 N N R -0.110 2.043 1.234 1.671 -1.180 -5.448 "C2'R" NGD 33 NGD "O2'R" RO2* O 0 0 N N N -1.233 1.908 0.378 1.856 -2.220 -6.385 "O2'R" NGD 34 NGD "O4'R" RO4* O 0 0 N N N 1.941 2.932 0.505 2.163 1.104 -5.055 "O4'R" NGD 35 NGD "C1'R" RC1* C 0 0 N N R 1.201 1.701 0.514 2.743 -0.111 -5.568 "C1'R" NGD 36 NGD N1 N1 N 1 1 Y N N 2.034 0.696 1.215 3.963 -0.510 -4.822 N1 NGD 37 NGD C6 C6 C 0 1 Y N N 3.384 0.696 1.024 4.943 -1.167 -5.468 C6 NGD 38 NGD C5 C5 C 0 1 Y N N 4.245 -0.205 1.666 6.095 -1.551 -4.798 C5 NGD 39 NGD C4 C4 C 0 1 Y N N 3.652 -1.155 2.506 6.217 -1.244 -3.446 C4 NGD 40 NGD C2 C2 C 0 1 Y N N 1.459 -0.220 2.021 4.064 -0.205 -3.515 C2 NGD 41 NGD C3 C3 C 0 1 Y N N 2.253 -1.163 2.681 5.193 -0.565 -2.793 C3 NGD 42 NGD C7 C7 C 0 1 N N N 1.634 -2.172 3.591 5.302 -0.237 -1.382 C7 NGD 43 NGD N7 N7 N 0 1 N N N 0.389 -2.392 3.651 4.241 0.444 -0.790 N7 NGD 44 NGD O7 O7 O 0 1 N N N 2.439 -2.846 4.382 6.312 -0.537 -0.721 O7 NGD 45 NGD H8A H8A H 0 1 N N N 8.958 -3.382 3.722 -0.510 -2.628 -2.157 H8A NGD 46 NGD H2A1 1H2A H 0 0 N N N 8.914 3.510 3.705 4.035 -6.728 1.332 H2A1 NGD 47 NGD H2A2 2H2A H 0 0 N N N 10.009 4.073 2.428 4.818 -7.422 -0.071 H2A2 NGD 48 NGD HN1A HN1A H 0 0 N N N 11.049 2.221 1.216 4.069 -7.139 -2.123 HN1A NGD 49 NGD "H1'" H1* H 0 1 N N N 7.711 -2.300 5.429 0.504 -3.862 1.242 "H1'" NGD 50 NGD "H2'" H2* H 0 1 N N N 8.437 0.703 5.900 1.250 -1.182 -0.064 "H2'" NGD 51 NGD HO2 HO2 H 0 1 N N N 9.938 -0.896 6.441 2.709 -2.825 1.036 HO2 NGD 52 NGD "H3'" H3* H 0 1 N N N 6.652 0.718 7.539 0.246 -0.038 1.866 "H3'" NGD 53 NGD HO3 HO3 H 0 1 N N N 6.789 -2.144 7.437 1.009 -1.477 3.410 HO3 NGD 54 NGD "H4'" H4* H 0 1 N N N 5.070 -1.380 6.244 -2.044 -1.619 1.844 "H4'" NGD 55 NGD H51 1H5 H 0 1 N N N 4.217 0.699 6.977 -2.664 -0.763 -0.374 H51 NGD 56 NGD H52 2H5 H 0 1 N N N 3.836 0.193 5.218 -0.964 -0.365 -0.732 H52 NGD 57 NGD HO1A HO1A H 0 0 N N N 4.171 3.286 8.197 -4.551 1.593 -0.373 HO1A NGD 58 NGD HO2B HO2B H 0 0 N N N 6.165 3.759 2.547 0.880 1.183 0.343 HO2B NGD 59 NGD "H5'1" 1H5* H 0 0 N N N 1.899 4.132 3.633 0.811 0.171 -2.979 "H5'1" NGD 60 NGD "H5'2" 2H5* H 0 0 N N N 1.735 2.381 3.147 -0.782 0.817 -3.452 "H5'2" NGD 61 NGD "HC4'" HC4* H 0 0 N N N 1.721 4.847 1.391 0.279 1.800 -5.515 "HC4'" NGD 62 NGD "HC3'" HC3* H 0 0 N N N -0.441 3.724 2.591 -0.502 -0.863 -5.350 "HC3'" NGD 63 NGD "HO3'" HO3* H 0 0 N N N -0.915 5.199 1.107 -0.097 0.761 -7.184 "HO3'" NGD 64 NGD "HC2'" HC2* H 0 0 N N N -0.247 1.370 2.093 1.660 -1.608 -4.439 "HC2'" NGD 65 NGD "HO2'" HO2* H 0 0 N N N -2.027 1.878 0.899 1.159 -2.130 -7.059 "HO2'" NGD 66 NGD "HC1'" HC1* H 0 0 N N N 0.966 1.277 -0.474 3.081 0.052 -6.597 "HC1'" NGD 67 NGD H6 H6 H 0 1 N N N 3.809 1.423 0.348 4.780 -1.371 -6.520 H6 NGD 68 NGD H5 H5 H 0 1 N N N 5.314 -0.168 1.520 6.886 -2.080 -5.318 H5 NGD 69 NGD H4 H4 H 0 1 N N N 4.265 -1.881 3.019 7.115 -1.540 -2.909 H4 NGD 70 NGD H2 H2 H 0 1 N N N 0.388 -0.225 2.156 3.224 0.325 -3.081 H2 NGD 71 NGD HN71 1HN7 H 0 0 N N N 0.197 -3.105 4.325 3.434 0.689 -1.353 HN71 NGD 72 NGD HN72 2HN7 H 0 0 N N N -0.303 -1.921 3.104 4.257 0.700 0.192 HN72 NGD 73 # # 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 NGD O6A C6A DOUB N N 1 NGD C6A N1A SING N N 2 NGD C6A C5A SING N N 3 NGD C5A N7A SING Y N 4 NGD C5A C4A DOUB Y N 5 NGD N7A C8A DOUB Y N 6 NGD C8A N9A SING Y N 7 NGD C8A H8A SING N N 8 NGD N9A C4A SING Y N 9 NGD N9A "C1'" SING N N 10 NGD C4A N3A SING N N 11 NGD N3A C2A DOUB N N 12 NGD C2A N1A SING N N 13 NGD C2A N2A SING N N 14 NGD N2A H2A1 SING N N 15 NGD N2A H2A2 SING N N 16 NGD N1A HN1A SING N N 17 NGD "C1'" "O4'" SING N N 18 NGD "C1'" "C2'" SING N N 19 NGD "C1'" "H1'" SING N N 20 NGD "O4'" "C4'" SING N N 21 NGD "C2'" "O2'" SING N N 22 NGD "C2'" "C3'" SING N N 23 NGD "C2'" "H2'" SING N N 24 NGD "O2'" HO2 SING N N 25 NGD "C3'" "C4'" SING N N 26 NGD "C3'" "O3'" SING N N 27 NGD "C3'" "H3'" SING N N 28 NGD "O3'" HO3 SING N N 29 NGD "C4'" "C5'" SING N N 30 NGD "C4'" "H4'" SING N N 31 NGD "C5'" "O5'" SING N N 32 NGD "C5'" H51 SING N N 33 NGD "C5'" H52 SING N N 34 NGD "O5'" PA SING N N 35 NGD PA O3 SING N N 36 NGD PA O2A DOUB N N 37 NGD PA O1A SING N N 38 NGD O1A HO1A SING N N 39 NGD O3 PB SING N N 40 NGD PB "O5'R" SING N N 41 NGD PB O1B DOUB N N 42 NGD PB O2B SING N N 43 NGD O2B HO2B SING N N 44 NGD "O5'R" "C5'R" SING N N 45 NGD "C5'R" "C4'R" SING N N 46 NGD "C5'R" "H5'1" SING N N 47 NGD "C5'R" "H5'2" SING N N 48 NGD "C4'R" "O4'R" SING N N 49 NGD "C4'R" "C3'R" SING N N 50 NGD "C4'R" "HC4'" SING N N 51 NGD "C3'R" "O3'R" SING N N 52 NGD "C3'R" "C2'R" SING N N 53 NGD "C3'R" "HC3'" SING N N 54 NGD "O3'R" "HO3'" SING N N 55 NGD "C2'R" "O2'R" SING N N 56 NGD "C2'R" "C1'R" SING N N 57 NGD "C2'R" "HC2'" SING N N 58 NGD "O2'R" "HO2'" SING N N 59 NGD "O4'R" "C1'R" SING N N 60 NGD "C1'R" N1 SING N N 61 NGD "C1'R" "HC1'" SING N N 62 NGD N1 C6 DOUB Y N 63 NGD N1 C2 SING Y N 64 NGD C6 C5 SING Y N 65 NGD C6 H6 SING N N 66 NGD C5 C4 DOUB Y N 67 NGD C5 H5 SING N N 68 NGD C4 C3 SING Y N 69 NGD C4 H4 SING N N 70 NGD C2 C3 DOUB Y N 71 NGD C2 H2 SING N N 72 NGD C3 C7 SING N N 73 NGD C7 N7 SING N N 74 NGD C7 O7 DOUB N N 75 NGD N7 HN71 SING N N 76 NGD N7 HN72 SING N N 77 # # 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 NGD SMILES_CANONICAL CACTVS 3.341 "NC(=O)c1ccc[n+](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(=O)NC(=Nc45)N)[C@@H](O)[C@H]2O" NGD SMILES CACTVS 3.341 "NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)NC(=Nc45)N)[CH](O)[CH]2O" NGD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4N=C(NC5=O)N)O)O)O)O)C(=O)N" NGD SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4N=C(NC5=O)N)O)O)O)O)C(=O)N" NGD InChI InChI 1.03 "InChI=1S/C21H27N7O15P2/c22-16(33)8-2-1-3-27(4-8)19-14(31)12(29)9(41-19)5-39-44(35,36)43-45(37,38)40-6-10-13(30)15(32)20(42-10)28-7-24-11-17(28)25-21(23)26-18(11)34/h1-4,7,9-10,12-15,19-20,29-32H,5-6H2,(H6-,22,23,25,26,33,34,35,36,37,38)/p+1/t9-,10-,12-,13-,14-,15-,19-,20-/m1/s1" NGD InChIKey InChI 1.03 NCFRZZVNRVEQJK-NAJQWHGHSA-O # _pdbx_chem_comp_identifier.comp_id NGD _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-aminocarbonylpyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-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 NGD "Create component" 2006-12-12 PDBJ NGD "Modify descriptor" 2011-06-04 RCSB NGD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id NGD _pdbx_chem_comp_synonyms.name "NICOTINAMIDE GUANINE DINUCLEOTIDE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##