data_NDE # _chem_comp.id NDE _chem_comp.name "ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) P'-5'-ESTER WITH 3-(AMINOCARBONYL)-4-(1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPYL)-1-BETA-D-RIBOFURANOSYLPYRIDINIUM INNER SALT" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H32 N7 O20 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "NAD WITH (1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPANE)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-11-11 _chem_comp.pdbx_modified_date 2021-03-01 _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 831.467 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NDE _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1N1E _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.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 NDE O7N NO7 O 0 1 N N N 27.612 18.620 -15.613 -5.883 0.314 0.065 O7N NDE 1 NDE C7N NC7 C 0 1 N N N 28.370 18.307 -16.531 -4.908 -0.171 -0.534 C7N NDE 2 NDE N7N NN7 N 0 1 N N N 28.028 17.270 -17.293 -4.717 0.059 -1.893 N7N NDE 3 NDE C3N NC3 C 0 1 Y N N 29.616 19.063 -16.767 -3.917 -0.978 0.161 C3N NDE 4 NDE C4N NC4 C 0 1 Y N N 29.959 20.272 -15.897 -4.036 -2.361 0.260 C4N NDE 5 NDE C5N NC5 C 0 1 Y N N 31.074 21.096 -16.458 -3.065 -3.095 0.934 C5N NDE 6 NDE C6N NC6 C 0 1 Y N N 31.991 20.537 -17.259 -1.990 -2.422 1.497 C6N NDE 7 NDE C2N NC2 C 0 1 Y N N 30.408 18.622 -17.783 -2.820 -0.359 0.744 C2N NDE 8 NDE N1N NN1 N 1 1 Y N N 31.669 19.317 -17.982 -1.890 -1.084 1.392 N1N NDE 9 NDE C1D NC1* C 0 1 N N R 32.628 18.846 -18.985 -0.729 -0.392 2.006 C1D NDE 10 NDE C2D NC2* C 0 1 N N R 33.189 17.448 -18.810 0.394 -0.237 0.995 C2D NDE 11 NDE O2D NO2* O 0 1 N N N 34.260 17.507 -17.900 1.187 -1.402 0.903 O2D NDE 12 NDE C3D NC3* C 0 1 N N S 33.591 17.087 -20.249 1.147 0.950 1.561 C3D NDE 13 NDE O3D NO3* O 0 1 N N N 34.937 17.457 -20.467 1.951 0.524 2.661 O3D NDE 14 NDE O4D NO4* O 0 1 N N N 31.969 18.813 -20.227 -1.059 0.936 2.452 O4D NDE 15 NDE C4D NC4* C 0 1 N N R 32.730 17.992 -21.130 0.018 1.830 2.089 C4D NDE 16 NDE C5D NC5* C 0 1 N N N 31.681 17.276 -21.940 -0.504 2.814 1.051 C5D NDE 17 NDE O5D NO5* O 0 1 N N N 31.138 16.312 -21.073 -1.552 3.577 1.624 O5D NDE 18 NDE PN NP P 0 1 N N N 29.572 15.980 -21.028 -2.296 4.718 0.718 PN NDE 19 NDE O1N NO1 O 0 1 N N N 29.206 15.911 -19.574 -3.558 5.143 1.436 O1N NDE 20 NDE O2N NO2 O -1 1 N N N 28.806 16.888 -21.983 -1.280 5.747 0.272 O2N NDE 21 NDE PA AP P 0 1 N N S 28.251 13.239 -22.141 -3.495 4.192 -1.937 PA NDE 22 NDE O1A AO1 O 0 1 N N N 28.890 12.143 -21.393 -2.818 5.247 -2.763 O1A NDE 23 NDE O3 O3 O 0 1 N N N 29.256 14.222 -21.583 -2.714 3.809 -0.573 O3 NDE 24 NDE O2A AO2 O 0 1 N N N 27.204 14.070 -21.491 -3.656 2.765 -2.682 O2A NDE 25 NDE O5B AO5* O 0 1 N N N 28.641 13.441 -23.657 -4.995 4.566 -1.457 O5B NDE 26 NDE C5B AC5* C 0 1 N N N 29.552 12.636 -24.360 -5.736 3.649 -0.671 C5B NDE 27 NDE C4B AC4* C 0 1 N N R 29.961 13.479 -25.535 -7.098 4.257 -0.368 C4B NDE 28 NDE O4B AO4* O 0 1 N N N 31.084 12.780 -26.125 -7.792 4.467 -1.620 O4B NDE 29 NDE C1B AC1* C 0 1 N N R 30.702 12.319 -27.398 -8.945 3.605 -1.663 C1B NDE 30 NDE C2B AC2* C 0 1 N N R 29.188 12.300 -27.426 -8.722 2.547 -0.593 C2B NDE 31 NDE O2B AO2* O 0 1 N N N 28.772 12.368 -28.757 -9.940 2.000 -0.130 O2B NDE 32 NDE C3B AC3* C 0 1 N N S 28.893 13.564 -26.611 -7.986 3.341 0.468 C3B NDE 33 NDE O3B AO3* O 0 1 N N N 29.113 14.692 -27.411 -8.919 4.142 1.195 O3B NDE 34 NDE N9A AN9 N 0 1 Y N N 31.362 11.039 -27.551 -9.106 3.064 -3.010 N9A NDE 35 NDE C8A AC8 C 0 1 Y N N 31.145 9.891 -26.836 -8.096 2.764 -3.887 C8A NDE 36 NDE N7A AN7 N 0 1 Y N N 31.952 8.941 -27.267 -8.551 2.292 -5.029 N7A NDE 37 NDE C5A AC5 C 0 1 Y N N 32.742 9.472 -28.277 -9.916 2.285 -4.887 C5A NDE 38 NDE C6A AC6 C 0 1 Y N N 33.777 8.956 -29.080 -10.946 1.901 -5.740 C6A NDE 39 NDE N6A AN6 N 0 1 N N N 34.166 7.685 -28.940 -10.666 1.406 -7.026 N6A NDE 40 NDE C4A AC4 C 0 1 Y N N 32.367 10.788 -28.446 -10.282 2.762 -3.639 C4A NDE 41 NDE N3A AN3 N 0 1 Y N N 32.972 11.556 -29.367 -11.526 2.897 -3.154 N3A NDE 42 NDE C2A AC2 C 0 1 Y N N 33.948 11.050 -30.134 -12.435 2.494 -4.068 C2A NDE 43 NDE N1A AN1 N 0 1 Y N N 34.348 9.769 -29.997 -12.228 2.010 -5.316 N1A NDE 44 NDE P P P 0 1 N N N 31.261 15.254 -13.397 -8.236 -3.238 3.864 P NDE 45 NDE O1P O1P O 0 1 N N N 32.006 15.287 -14.706 -8.983 -4.212 4.728 O1P NDE 46 NDE O2P O2P O 0 1 N N N 32.013 14.748 -12.210 -9.146 -2.104 3.156 O2P NDE 47 NDE O3P O3P O 0 1 N N N 29.820 14.912 -13.511 -7.099 -2.380 4.628 O3P NDE 48 NDE O1 O1 O 0 1 N N N 31.231 16.818 -13.023 -7.424 -3.905 2.630 O1 NDE 49 NDE C1 C1 C 0 1 N N N 30.367 17.666 -13.794 -6.693 -3.059 1.765 C1 NDE 50 NDE C2 C2 C 0 1 N N N 30.924 19.034 -14.048 -6.008 -3.870 0.681 C2 NDE 51 NDE O2 O2 O 0 1 N N N 32.121 19.353 -14.066 -6.112 -5.096 0.627 O2 NDE 52 NDE C3 C3 C 0 1 N N R 29.942 20.100 -14.337 -5.195 -3.081 -0.348 C3 NDE 53 NDE O31 O31 O 0 1 N N N ? ? ? -4.718 -3.973 -1.351 O31 NDE 54 NDE H71N NH71 H 0 0 N N N 27.167 16.747 -17.130 -3.905 -0.336 -2.354 H71N NDE 55 NDE H72N NH72 H 0 0 N N N 28.656 17.010 -18.053 -5.373 0.614 -2.433 H72N NDE 56 NDE H5N NH5 H 0 1 N N N 31.228 22.172 -16.271 -3.138 -4.174 1.024 H5N NDE 57 NDE H6N NH6 H 0 1 N N N 32.962 21.055 -17.320 -1.198 -2.927 2.036 H6N NDE 58 NDE H2N NH2 H 0 1 N N N 30.057 17.773 -18.393 -2.655 0.712 0.712 H2N NDE 59 NDE H1D NH1* H 0 1 N N N 33.483 19.554 -18.890 -0.455 -1.010 2.867 H1D NDE 60 NDE H2D NH2* H 0 1 N N N 32.501 16.680 -18.384 -0.006 0.000 0.003 H2D NDE 61 NDE HO2N NHO2 H 0 0 N N N 34.611 16.631 -17.790 1.511 -1.460 -0.013 HO2N NDE 62 NDE H3D NH3* H 0 1 N N N 33.463 15.998 -20.454 1.804 1.442 0.840 H3D NDE 63 NDE HO3N NHO3 H 0 0 N N N 35.185 17.233 -21.356 2.515 -0.190 2.327 HO3N NDE 64 NDE H4D NH4* H 0 1 N N N 33.424 18.513 -21.829 0.312 2.377 2.991 H4D NDE 65 NDE H51N NH51 H 0 0 N N N 30.920 17.954 -22.391 -0.892 2.281 0.178 H51N NDE 66 NDE H52N NH52 H 0 0 N N N 32.063 16.854 -22.898 0.292 3.492 0.732 H52N NDE 67 NDE HOA2 2HOA H 0 0 N N N 26.791 14.777 -21.973 -3.983 2.747 -3.607 HOA2 NDE 68 NDE H51A AH51 H 0 0 N N N 30.404 12.266 -23.744 -5.856 2.717 -1.225 H51A NDE 69 NDE H52A AH52 H 0 0 N N N 29.155 11.630 -24.635 -5.197 3.455 0.258 H52A NDE 70 NDE H4B AH4* H 0 1 N N N 30.171 14.516 -25.184 -6.961 5.236 0.102 H4B NDE 71 NDE H1B AH1* H 0 1 N N N 31.004 12.950 -28.265 -9.844 4.203 -1.482 H1B NDE 72 NDE H2B AH2* H 0 1 N N N 28.671 11.400 -27.016 -8.088 1.734 -0.968 H2B NDE 73 NDE HO2A AHO2 H 0 0 N N N 27.822 12.356 -28.774 -10.276 1.411 -0.828 HO2A NDE 74 NDE H3B AH3* H 0 1 N N N 27.851 13.638 -26.220 -7.446 2.722 1.189 H3B NDE 75 NDE HO3A AHO3 H 0 0 N N N 28.444 14.745 -28.084 -8.534 4.280 2.073 HO3A NDE 76 NDE H8A AH8 H 0 1 N N N 30.416 9.750 -26.020 -7.054 2.910 -3.637 H8A NDE 77 NDE H61A AH61 H 0 0 N N N 34.915 7.311 -29.521 -9.715 1.360 -7.340 H61A NDE 78 NDE H62A AH62 H 0 0 N N N 33.347 7.085 -29.045 -11.423 1.194 -7.648 H62A NDE 79 NDE H2A AH2 H 0 1 N N N 34.428 11.696 -30.887 -13.473 2.568 -3.761 H2A NDE 80 NDE HOP2 2HOP H 0 0 N N N 31.543 14.727 -11.384 -9.789 -1.603 3.701 HOP2 NDE 81 NDE HOP3 3HOP H 0 0 N N N 29.350 14.891 -12.685 -7.323 -1.946 5.479 HOP3 NDE 82 NDE H11 1H1 H 0 1 N N N 30.088 17.172 -14.754 -7.391 -2.359 1.299 H11 NDE 83 NDE H12 2H1 H 0 1 N N N 29.360 17.735 -13.319 -5.954 -2.509 2.352 H12 NDE 84 NDE H31 1H3 H 0 1 N N N 30.030 21.139 -13.942 -5.888 -2.387 -0.850 H31 NDE 85 NDE H311 1H31 H 0 0 N N N -0.010 -0.104 0.944 -5.345 -4.712 -1.385 H311 NDE 86 # # 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 NDE O7N C7N DOUB N N 1 NDE C7N N7N SING N N 2 NDE C7N C3N SING N N 3 NDE N7N H71N SING N N 4 NDE N7N H72N SING N N 5 NDE C3N C4N SING Y N 6 NDE C3N C2N DOUB Y N 7 NDE C4N C5N DOUB Y N 8 NDE C4N C3 SING N N 9 NDE C5N C6N SING Y N 10 NDE C5N H5N SING N N 11 NDE C6N N1N DOUB Y N 12 NDE C6N H6N SING N N 13 NDE C2N N1N SING Y N 14 NDE C2N H2N SING N N 15 NDE N1N C1D SING N N 16 NDE C1D C2D SING N N 17 NDE C1D O4D SING N N 18 NDE C1D H1D SING N N 19 NDE C2D O2D SING N N 20 NDE C2D C3D SING N N 21 NDE C2D H2D SING N N 22 NDE O2D HO2N SING N N 23 NDE C3D O3D SING N N 24 NDE C3D C4D SING N N 25 NDE C3D H3D SING N N 26 NDE O3D HO3N SING N N 27 NDE O4D C4D SING N N 28 NDE C4D C5D SING N N 29 NDE C4D H4D SING N N 30 NDE C5D O5D SING N N 31 NDE C5D H51N SING N N 32 NDE C5D H52N SING N N 33 NDE O5D PN SING N N 34 NDE PN O1N DOUB N N 35 NDE PN O2N SING N N 36 NDE PN O3 SING N N 37 NDE PA O1A DOUB N N 38 NDE PA O3 SING N N 39 NDE PA O2A SING N N 40 NDE PA O5B SING N N 41 NDE O2A HOA2 SING N N 42 NDE O5B C5B SING N N 43 NDE C5B C4B SING N N 44 NDE C5B H51A SING N N 45 NDE C5B H52A SING N N 46 NDE C4B O4B SING N N 47 NDE C4B C3B SING N N 48 NDE C4B H4B SING N N 49 NDE O4B C1B SING N N 50 NDE C1B C2B SING N N 51 NDE C1B N9A SING N N 52 NDE C1B H1B SING N N 53 NDE C2B O2B SING N N 54 NDE C2B C3B SING N N 55 NDE C2B H2B SING N N 56 NDE O2B HO2A SING N N 57 NDE C3B O3B SING N N 58 NDE C3B H3B SING N N 59 NDE O3B HO3A SING N N 60 NDE N9A C8A SING Y N 61 NDE N9A C4A SING Y N 62 NDE C8A N7A DOUB Y N 63 NDE C8A H8A SING N N 64 NDE N7A C5A SING Y N 65 NDE C5A C6A DOUB Y N 66 NDE C5A C4A SING Y N 67 NDE C6A N6A SING N N 68 NDE C6A N1A SING Y N 69 NDE N6A H61A SING N N 70 NDE N6A H62A SING N N 71 NDE C4A N3A DOUB Y N 72 NDE N3A C2A SING Y N 73 NDE C2A N1A DOUB Y N 74 NDE C2A H2A SING N N 75 NDE P O1P DOUB N N 76 NDE P O2P SING N N 77 NDE P O3P SING N N 78 NDE P O1 SING N N 79 NDE O2P HOP2 SING N N 80 NDE O3P HOP3 SING N N 81 NDE O1 C1 SING N N 82 NDE C1 C2 SING N N 83 NDE C1 H11 SING N N 84 NDE C1 H12 SING N N 85 NDE C2 O2 DOUB N N 86 NDE C2 C3 SING N N 87 NDE C3 O31 SING N N 88 NDE C3 H31 SING N N 89 NDE O31 H311 SING N N 90 # # 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 NDE SMILES_CANONICAL CACTVS 3.341 "NC(=O)c1c[n+](ccc1[C@@H](O)C(=O)CO[P](O)(O)=O)[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" NDE SMILES CACTVS 3.341 "NC(=O)c1c[n+](ccc1[CH](O)C(=O)CO[P](O)(O)=O)[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" NDE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1c[n+](cc(c1[C@H](C(=O)COP(=O)(O)O)O)C(=O)N)[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)n4cnc5c4ncnc5N)O)O)O)O" NDE SMILES "OpenEye OEToolkits" 1.5.0 "c1c[n+](cc(c1C(C(=O)COP(=O)(O)O)O)C(=O)N)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O" NDE InChI InChI 1.03 "InChI=1S/C24H32N7O20P3/c25-20-14-22(28-7-27-20)31(8-29-14)24-19(37)17(35)13(50-24)6-48-54(44,45)51-53(42,43)47-5-12-16(34)18(36)23(49-12)30-2-1-9(10(3-30)21(26)38)15(33)11(32)4-46-52(39,40)41/h1-3,7-8,12-13,15-19,23-24,33-37H,4-6H2,(H7-,25,26,27,28,38,39,40,41,42,43,44,45)/t12-,13-,15?,16-,17-,18-,19-,23-,24-/m1/s1" NDE InChIKey InChI 1.03 IVZPTIKSOMOSEU-WPIGAQFXSA-N # _pdbx_chem_comp_identifier.comp_id NDE _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-4-[(1R)-1-hydroxy-2-oxo-3-phosphonooxy-propyl]pyridin-1-ium-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] 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 NDE "Create component" 2002-11-11 RCSB NDE "Modify descriptor" 2011-06-04 RCSB NDE "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id NDE _pdbx_chem_comp_synonyms.name "NAD WITH (1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPANE)" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##