data_NDA # _chem_comp.id NDA _chem_comp.name 3-AMINOMETHYL-PYRIDINIUM-ADENINE-DINUCLEOTIDE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H29 N7 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-02-03 _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 649.442 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NDA _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 1EBU _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 NDA PA AP P 0 1 N N S 41.067 21.183 70.797 -0.660 -0.887 -0.574 PA NDA 1 NDA O1A AO1 O 0 1 N N N 40.609 22.504 71.369 -0.998 -0.022 -1.727 O1A NDA 2 NDA O2A AO2 O 0 1 N N N 39.961 20.259 70.335 -0.031 -2.270 -1.106 O2A NDA 3 NDA O5B AO5* O 0 1 N N N 41.992 20.376 71.890 -1.993 -1.194 0.275 O5B NDA 4 NDA C5B AC5* C 0 1 N N N 42.964 21.111 72.687 -2.943 -1.750 -0.636 C5B NDA 5 NDA C4B AC4* C 0 1 N N R 43.527 20.243 73.820 -4.241 -2.068 0.110 C4B NDA 6 NDA O4B AO4* O 0 1 N N N 44.485 21.110 74.488 -4.862 -0.848 0.550 O4B NDA 7 NDA C3B AC3* C 0 1 N N S 42.520 19.817 74.920 -5.230 -2.775 -0.836 C3B NDA 8 NDA O3B AO3* O 0 1 N N N 42.617 18.404 75.172 -5.568 -4.071 -0.338 O3B NDA 9 NDA C2B AC2* C 0 1 N N R 42.902 20.730 76.092 -6.477 -1.852 -0.835 C2B NDA 10 NDA O2B AO2* O 0 1 N N N 42.567 20.130 77.374 -7.680 -2.621 -0.799 O2B NDA 11 NDA C1B AC1* C 0 1 N N R 44.395 20.911 75.873 -6.290 -1.054 0.481 C1B NDA 12 NDA N9A AN9 N 0 1 Y N N 44.987 22.100 76.529 -6.993 0.229 0.415 N9A NDA 13 NDA C8A AC8 C 0 1 Y N N 44.794 23.422 76.186 -6.476 1.411 -0.026 C8A NDA 14 NDA N7A AN7 N 0 1 Y N N 45.502 24.275 76.934 -7.377 2.347 0.051 N7A NDA 15 NDA C5A AC5 C 0 1 Y N N 46.195 23.453 77.821 -8.526 1.827 0.545 C5A NDA 16 NDA C6A AC6 C 0 1 Y N N 47.123 23.763 78.856 -9.799 2.345 0.840 C6A NDA 17 NDA N6A AN6 N 0 1 N N N 47.511 24.994 79.204 -10.087 3.681 0.625 N6A NDA 18 NDA N1A AN1 N 0 1 Y N N 47.579 22.709 79.641 -10.720 1.521 1.330 N1A NDA 19 NDA C2A AC2 C 0 1 Y N N 47.229 21.434 79.239 -10.454 0.244 1.538 C2A NDA 20 NDA N3A AN3 N 0 1 Y N N 46.408 21.032 78.279 -9.277 -0.284 1.276 N3A NDA 21 NDA C4A AC4 C 0 1 Y N N 45.912 22.104 77.587 -8.296 0.460 0.779 C4A NDA 22 NDA O3 O3 O 0 1 N N N 42.084 21.489 69.612 0.412 -0.135 0.364 O3 NDA 23 NDA PN NP P 0 1 N N N 42.766 20.508 68.440 1.453 0.603 -0.618 PN NDA 24 NDA O1N NO1 O 0 1 N N N 41.641 20.074 67.544 0.833 1.923 -1.127 O1N NDA 25 NDA O2N NO2 O -1 1 N N N 43.457 19.357 69.170 1.767 -0.316 -1.819 O2N NDA 26 NDA O5D NO5* O 0 1 N N N 43.701 21.595 67.683 2.812 0.922 0.184 O5D NDA 27 NDA C5D NC5* C 0 1 N N N 45.112 21.529 67.925 3.733 1.465 -0.764 C5D NDA 28 NDA C4D NC4* C 0 1 N N R 45.824 22.609 67.134 5.053 1.792 -0.064 C4D NDA 29 NDA O4D NO4* O 0 1 N N N 45.812 22.231 65.710 5.698 0.580 0.385 O4D NDA 30 NDA C3D NC3* C 0 1 N N S 45.247 24.036 67.166 6.050 2.425 -1.059 C3D NDA 31 NDA O3D NO3* O 0 1 N N N 46.325 25.009 67.152 6.046 3.849 -0.935 O3D NDA 32 NDA C2D NC2* C 0 1 N N R 44.409 24.075 65.869 7.422 1.848 -0.636 C2D NDA 33 NDA O2D NO2* O 0 1 N N N 44.175 25.455 65.470 8.307 2.898 -0.241 O2D NDA 34 NDA C1D NC1* C 0 1 N N R 45.332 23.322 64.940 7.087 0.932 0.562 C1D NDA 35 NDA N1N NN1 N 1 1 Y N N 44.731 22.832 63.673 7.925 -0.269 0.535 N1N NDA 36 NDA C2N NC2 C 0 1 Y N N 43.546 22.069 63.607 8.966 -0.344 1.342 C2N NDA 37 NDA C3N NC3 C 0 1 Y N N 43.026 21.552 62.283 9.783 -1.459 1.339 C3N NDA 38 NDA C7N NC7 C 0 1 N N N 41.796 20.732 62.299 10.974 -1.534 2.259 C7N NDA 39 NDA N7N NN7 N 0 1 N N N 41.110 20.439 63.425 12.154 -0.983 1.578 N7N NDA 40 NDA C4N NC4 C 0 1 Y N N 43.762 21.918 61.007 9.489 -2.510 0.484 C4N NDA 41 NDA C5N NC5 C 0 1 Y N N 44.975 22.748 61.254 8.383 -2.398 -0.344 C5N NDA 42 NDA C6N NC6 C 0 1 Y N N 45.409 23.148 62.443 7.616 -1.249 -0.290 C6N NDA 43 NDA HOA2 2HOA H 0 0 N N N 40.249 19.428 69.975 0.174 -2.802 -0.325 HOA2 NDA 44 NDA H51A AH51 H 0 0 N N N 43.777 21.533 72.052 -3.148 -1.033 -1.431 H51A NDA 45 NDA H52A AH52 H 0 0 N N N 42.536 22.064 73.075 -2.540 -2.666 -1.068 H52A NDA 46 NDA H4B AH4* H 0 1 N N N 43.907 19.299 73.362 -4.028 -2.705 0.968 H4B NDA 47 NDA H3B AH3* H 0 1 N N N 41.442 19.942 74.663 -4.811 -2.850 -1.839 H3B NDA 48 NDA HO3A AHO3 H 0 0 N N N 42.000 18.143 75.845 -6.233 -4.437 -0.938 HO3A NDA 49 NDA H2B AH2* H 0 1 N N N 42.352 21.700 76.121 -6.469 -1.186 -1.698 H2B NDA 50 NDA HO2A AHO2 H 0 0 N N N 42.803 20.695 78.099 -7.737 -3.091 -1.642 HO2A NDA 51 NDA H1B AH1* H 0 1 N N N 44.943 20.037 76.297 -6.635 -1.637 1.335 H1B NDA 52 NDA H8A AH8 H 0 1 N N N 44.127 23.769 75.378 -5.468 1.550 -0.387 H8A NDA 53 NDA H61A AH61 H 0 0 N N N 48.175 25.216 79.945 -9.406 4.272 0.267 H61A NDA 54 NDA H62A AH62 H 0 0 N N N 46.661 25.521 79.406 -10.969 4.027 0.833 H62A NDA 55 NDA H2A AH2 H 0 1 N N N 47.685 20.587 79.779 -11.232 -0.390 1.937 H2A NDA 56 NDA H51N NH51 H 0 0 N N N 45.352 21.579 69.012 3.315 2.375 -1.196 H51N NDA 57 NDA H52N NH52 H 0 0 N N N 45.525 20.515 67.714 3.912 0.736 -1.555 H52N NDA 58 NDA H4D NH4* H 0 1 N N N 46.821 22.658 67.630 4.879 2.463 0.778 H4D NDA 59 NDA H3D NH3* H 0 1 N N N 44.647 24.277 68.074 5.809 2.131 -2.081 H3D NDA 60 NDA HO3N NHO3 H 0 0 N N N 45.969 25.889 67.171 6.684 4.187 -1.578 HO3N NDA 61 NDA H2D NH2* H 0 1 N N N 43.384 23.637 65.920 7.859 1.267 -1.449 H2D NDA 62 NDA HO2N NHO2 H 0 0 N N N 43.659 25.479 64.672 8.428 3.467 -1.013 HO2N NDA 63 NDA H1D NH1* H 0 1 N N N 46.122 24.022 64.584 7.226 1.469 1.501 H1D NDA 64 NDA H2N NH2 H 0 1 N N N 43.038 21.881 64.567 9.189 0.479 2.005 H2N NDA 65 NDA HC71 1HC7 H 0 0 N N N 41.077 21.200 61.586 11.162 -2.574 2.527 HC71 NDA 66 NDA HC72 2HC7 H 0 0 N N N 42.036 19.765 61.797 10.773 -0.957 3.162 HC72 NDA 67 NDA H71N NH71 H 0 0 N N N 40.261 19.873 63.436 11.977 0.001 1.443 H71N NDA 68 NDA H72N NH72 H 0 0 N N N 40.889 21.323 63.883 12.923 -1.053 2.228 H72N NDA 69 NDA H4N NH4 H 0 1 N N N 43.445 21.610 59.996 10.107 -3.396 0.464 H4N NDA 70 NDA H5N NH5 H 0 1 N N N 45.638 23.114 60.452 8.125 -3.197 -1.023 H5N NDA 71 NDA H6N NH6 H 0 1 N N N 46.335 23.744 62.408 6.753 -1.154 -0.933 H6N NDA 72 # 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 NDA PA O1A DOUB N N 1 NDA PA O2A SING N N 2 NDA PA O5B SING N N 3 NDA PA O3 SING N N 4 NDA O2A HOA2 SING N N 5 NDA O5B C5B SING N N 6 NDA C5B C4B SING N N 7 NDA C5B H51A SING N N 8 NDA C5B H52A SING N N 9 NDA C4B O4B SING N N 10 NDA C4B C3B SING N N 11 NDA C4B H4B SING N N 12 NDA O4B C1B SING N N 13 NDA C3B O3B SING N N 14 NDA C3B C2B SING N N 15 NDA C3B H3B SING N N 16 NDA O3B HO3A SING N N 17 NDA C2B O2B SING N N 18 NDA C2B C1B SING N N 19 NDA C2B H2B SING N N 20 NDA O2B HO2A SING N N 21 NDA C1B N9A SING N N 22 NDA C1B H1B SING N N 23 NDA N9A C8A SING Y N 24 NDA N9A C4A SING Y N 25 NDA C8A N7A DOUB Y N 26 NDA C8A H8A SING N N 27 NDA N7A C5A SING Y N 28 NDA C5A C6A SING Y N 29 NDA C5A C4A DOUB Y N 30 NDA C6A N6A SING N N 31 NDA C6A N1A DOUB Y N 32 NDA N6A H61A SING N N 33 NDA N6A H62A SING N N 34 NDA N1A C2A SING Y N 35 NDA C2A N3A DOUB Y N 36 NDA C2A H2A SING N N 37 NDA N3A C4A SING Y N 38 NDA O3 PN SING N N 39 NDA PN O1N DOUB N N 40 NDA PN O2N SING N N 41 NDA PN O5D SING N N 42 NDA O5D C5D SING N N 43 NDA C5D C4D SING N N 44 NDA C5D H51N SING N N 45 NDA C5D H52N SING N N 46 NDA C4D O4D SING N N 47 NDA C4D C3D SING N N 48 NDA C4D H4D SING N N 49 NDA O4D C1D SING N N 50 NDA C3D O3D SING N N 51 NDA C3D C2D SING N N 52 NDA C3D H3D SING N N 53 NDA O3D HO3N SING N N 54 NDA C2D O2D SING N N 55 NDA C2D C1D SING N N 56 NDA C2D H2D SING N N 57 NDA O2D HO2N SING N N 58 NDA C1D N1N SING N N 59 NDA C1D H1D SING N N 60 NDA N1N C2N SING Y N 61 NDA N1N C6N DOUB Y N 62 NDA C2N C3N DOUB Y N 63 NDA C2N H2N SING N N 64 NDA C3N C7N SING N N 65 NDA C3N C4N SING Y N 66 NDA C7N N7N SING N N 67 NDA C7N HC71 SING N N 68 NDA C7N HC72 SING N N 69 NDA N7N H71N SING N N 70 NDA N7N H72N SING N N 71 NDA C4N C5N DOUB Y N 72 NDA C4N H4N SING N N 73 NDA C5N C6N SING Y N 74 NDA C5N H5N SING N N 75 NDA C6N H6N SING N N 76 # 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 NDA SMILES_CANONICAL CACTVS 3.341 "NCc1ccc[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(N)ncnc45)[C@@H](O)[C@H]2O" NDA SMILES CACTVS 3.341 "NCc1ccc[n+](c1)[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" NDA 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)n4cnc5c4ncnc5N)O)O)O)O)CN" NDA SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)CN" NDA InChI InChI 1.03 ;InChI=1S/C21H29N7O13P2/c22-4-10-2-1-3-27(5-10)20-16(31)14(29)11(39-20)6-37-42(33,34)41-43(35,36)38-7-12-15(30)17(32)21(40-12)28-9-26-13-18(23)24-8-25-19(13)28/h1-3,5,8-9,11-12,14-17,20-21,29-32H,4,6-7,22H2,(H3-,23,24,25,33,34,35,36)/t11-,12-,14-,15-,16-,17-,20-,21-/m1/s1 ; NDA InChIKey InChI 1.03 HMCRLFVYYFBZEZ-PLEFRAQWSA-N # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NDA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-[3-(aminomethyl)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 NDA "Create component" 2000-02-03 RCSB NDA "Modify descriptor" 2011-06-04 RCSB #