data_DND # _chem_comp.id DND _chem_comp.name "NICOTINIC ACID ADENINE DINUCLEOTIDE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H27 N6 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms DEAMIDO-NAD+ _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2001-04-16 _chem_comp.pdbx_modified_date 2020-06-17 _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 665.418 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DND _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1KQO _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 DND PN PN P 0 1 N N N 9.531 43.089 14.197 1.491 -2.779 -1.073 PN DND 1 DND O11 O11 O 0 1 N N N 9.848 44.197 13.283 1.036 -3.219 -2.411 O11 DND 2 DND O12 O12 O 0 1 N N N 10.771 42.522 14.827 2.394 -3.934 -0.407 O12 DND 3 DND O3P O3P O 0 1 N N N 8.645 41.888 13.598 0.211 -2.493 -0.139 O3P DND 4 DND O5D O5D O 0 1 N N N 8.398 43.518 15.198 2.362 -1.433 -1.217 O5D DND 5 DND C5D C5D C 0 1 N N N 8.575 44.670 16.012 3.505 -1.333 -2.068 C5D DND 6 DND C4D C4D C 0 1 N N R 7.318 44.733 16.804 4.094 0.075 -1.969 C4D DND 7 DND O4D O4D O 0 1 N N N 7.684 45.319 18.056 4.624 0.292 -0.650 O4D DND 8 DND C3D C3D C 0 1 N N S 6.214 45.626 16.207 5.262 0.226 -2.962 C3D DND 9 DND O3D O3D O 0 1 N N N 4.884 45.130 16.586 4.991 1.272 -3.898 O3D DND 10 DND C2D C2D C 0 1 N N R 6.497 46.953 16.876 6.473 0.598 -2.071 C2D DND 11 DND O2D O2D O 0 1 N N N 5.330 47.810 16.880 7.270 1.609 -2.690 O2D DND 12 DND C1D C1D C 0 1 N N R 6.921 46.484 18.272 5.782 1.142 -0.795 C1D DND 13 DND N1N N1N N 1 1 Y N N 7.677 47.529 18.973 6.666 1.012 0.366 N1N DND 14 DND C6N C6N C 0 1 Y N N 9.016 47.909 18.640 6.840 -0.177 0.908 C6N DND 15 DND C5N C5N C 0 1 Y N N 9.689 48.889 19.277 7.666 -0.348 2.005 C5N DND 16 DND C4N C4N C 0 1 Y N N 9.036 49.678 20.415 8.318 0.749 2.539 C4N DND 17 DND C3N C3N C 0 1 Y N N 7.641 49.275 20.759 8.113 1.999 1.941 C3N DND 18 DND C2N C2N C 0 1 Y N N 7.026 48.204 20.013 7.268 2.086 0.834 C2N DND 19 DND C7N C7N C 0 1 N N N 6.788 49.878 21.808 8.784 3.204 2.471 C7N DND 20 DND O7N O7N O 0 1 N N N 5.533 49.483 22.097 8.599 4.283 1.944 O7N DND 21 DND O8N O8N O 0 1 N N N 7.329 50.790 22.403 9.600 3.106 3.538 O8N DND 22 DND PA PA P 0 1 N N N 9.061 40.513 12.883 -1.164 -3.279 0.146 PA DND 23 DND O13 O13 O 0 1 N N N 8.038 40.320 11.838 -1.680 -3.846 -1.121 O13 DND 24 DND O14 O14 O 0 1 N N N 10.471 40.510 12.352 -0.895 -4.470 1.196 O14 DND 25 DND O5B O5B O 0 1 N N N 8.891 39.305 13.940 -2.249 -2.259 0.758 O5B DND 26 DND C5B C5B C 0 1 N N N 7.576 39.005 14.542 -3.604 -2.630 1.020 C5B DND 27 DND C4B C4B C 0 1 N N R 7.875 38.153 15.786 -4.359 -1.429 1.596 C4B DND 28 DND O4B O4B O 0 1 N N N 8.748 37.021 15.472 -4.540 -0.416 0.583 O4B DND 29 DND C3B C3B C 0 1 N N S 8.591 38.909 16.912 -5.791 -1.840 2.004 C3B DND 30 DND O3B O3B O 0 1 N N N 7.867 38.790 18.163 -5.858 -2.095 3.408 O3B DND 31 DND C2B C2B C 0 1 N N R 9.975 38.255 16.846 -6.653 -0.611 1.636 C2B DND 32 DND O2B O2B O 0 1 N N N 10.700 38.368 18.082 -7.278 -0.071 2.802 O2B DND 33 DND C1B C1B C 0 1 N N R 9.622 36.802 16.468 -5.639 0.396 1.049 C1B DND 34 DND N9A N9A N 0 1 Y N N 10.748 36.079 15.888 -6.239 1.131 -0.067 N9A DND 35 DND C4A C4A C 0 1 Y N N 11.193 34.853 16.273 -6.963 2.293 0.022 C4A DND 36 DND N3A N3A N 0 1 Y N N 10.690 34.069 17.252 -7.343 3.088 1.017 N3A DND 37 DND C2A C2A C 0 1 Y N N 11.351 32.929 17.374 -8.055 4.169 0.777 C2A DND 38 DND N1A N1A N 0 1 Y N N 12.433 32.502 16.636 -8.424 4.519 -0.441 N1A DND 39 DND C6A C6A C 0 1 Y N N 12.928 33.326 15.642 -8.090 3.787 -1.499 C6A DND 40 DND C5A C5A C 0 1 Y N N 12.276 34.579 15.444 -7.330 2.623 -1.294 C5A DND 41 DND N7A N7A N 0 1 Y N N 12.525 35.601 14.552 -6.822 1.662 -2.103 N7A DND 42 DND C8A C8A C 0 1 Y N N 11.565 36.485 14.865 -6.176 0.789 -1.385 C8A DND 43 DND N6A N6A N 0 1 N N N 13.982 32.905 14.923 -8.483 4.161 -2.772 N6A DND 44 DND H1 H1 H 0 1 N N N 11.532 42.994 14.510 2.727 -3.713 0.474 H1 DND 45 DND H2 H2 H 0 1 N N N 9.449 44.556 16.670 4.254 -2.063 -1.758 H2 DND 46 DND H3 H3 H 0 1 N N N 8.696 45.572 15.395 3.210 -1.532 -3.099 H3 DND 47 DND H4 H4 H 0 1 N N N 6.919 43.719 16.952 3.323 0.815 -2.184 H4 DND 48 DND H5 H5 H 0 1 N N N 6.324 45.702 15.115 5.444 -0.714 -3.484 H5 DND 49 DND H6 H6 H 0 1 N N N 4.217 45.692 16.210 5.694 1.410 -4.548 H6 DND 50 DND H7 H7 H 0 1 N N N 7.344 47.449 16.380 7.073 -0.283 -1.844 H7 DND 51 DND H8 H8 H 0 1 N N N 5.542 48.632 17.306 7.651 1.345 -3.539 H8 DND 52 DND H9 H9 H 0 1 N N N 6.016 46.242 18.848 5.480 2.180 -0.935 H9 DND 53 DND H10 H10 H 0 1 N N N 9.513 47.384 17.838 6.330 -1.032 0.489 H10 DND 54 DND H11 H11 H 0 1 N N N 10.701 49.120 18.981 7.800 -1.327 2.440 H11 DND 55 DND H12 H12 H 0 1 N N N 9.551 50.473 20.934 8.968 0.645 3.396 H12 DND 56 DND H13 H13 H 0 1 N N N 6.019 47.910 20.268 7.103 3.042 0.360 H13 DND 57 DND H14 H14 H 0 1 N N N 6.735 51.138 23.058 10.016 3.922 3.848 H14 DND 58 DND H15 H15 H 0 1 N N N 10.455 40.381 11.411 -0.555 -4.171 2.050 H15 DND 59 DND H16 H16 H 0 1 N N N 7.064 39.935 14.828 -4.081 -2.947 0.093 H16 DND 60 DND H17 H17 H 0 1 N N N 6.949 38.444 13.834 -3.624 -3.450 1.738 H17 DND 61 DND H18 H18 H 0 1 N N N 6.920 37.774 16.179 -3.822 -1.020 2.452 H18 DND 62 DND H19 H19 H 0 1 N N N 8.683 39.968 16.629 -6.112 -2.717 1.442 H19 DND 63 DND H20 H20 H 0 1 N N N 8.329 39.265 18.843 -6.735 -2.357 3.720 H20 DND 64 DND H21 H21 H 0 1 N N N 10.548 38.709 16.024 -7.402 -0.880 0.891 H21 DND 65 DND H22 H22 H 0 1 N N N 10.886 39.283 18.258 -7.880 -0.684 3.245 H22 DND 66 DND H23 H23 H 0 1 N N N 9.192 36.270 17.330 -5.300 1.087 1.821 H23 DND 67 DND H24 H24 H 0 1 N N N 11.001 32.255 18.142 -8.347 4.793 1.609 H24 DND 68 DND H25 H25 H 0 1 N N N 11.447 37.431 14.357 -5.671 -0.082 -1.776 H25 DND 69 DND H26 H26 H 0 1 N N N 14.263 31.999 15.241 -9.007 4.967 -2.900 H26 DND 70 DND H27 H27 H 0 1 N N N 13.728 32.855 13.957 -8.233 3.618 -3.536 H27 DND 71 # # 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 DND O13 PA DOUB N N 1 DND O14 PA SING N N 2 DND PA O3P SING N N 3 DND PA O5B SING N N 4 DND O11 PN DOUB N N 5 DND O3P PN SING N N 6 DND O5B C5B SING N N 7 DND PN O12 SING N N 8 DND PN O5D SING N N 9 DND C5B C4B SING N N 10 DND N7A C8A DOUB Y N 11 DND N7A C5A SING Y N 12 DND C8A N9A SING Y N 13 DND N6A C6A SING N N 14 DND O5D C5D SING N N 15 DND C5A C6A SING Y N 16 DND C5A C4A DOUB Y N 17 DND O4B C4B SING N N 18 DND O4B C1B SING N N 19 DND C6A N1A DOUB Y N 20 DND C4B C3B SING N N 21 DND N9A C4A SING Y N 22 DND N9A C1B SING N N 23 DND C5D C4D SING N N 24 DND C3D O3D SING N N 25 DND C3D C4D SING N N 26 DND C3D C2D SING N N 27 DND C4A N3A SING Y N 28 DND C1B C2B SING N N 29 DND N1A C2A SING Y N 30 DND C4D O4D SING N N 31 DND C2B C3B SING N N 32 DND C2B O2B SING N N 33 DND C2D O2D SING N N 34 DND C2D C1D SING N N 35 DND C3B O3B SING N N 36 DND N3A C2A DOUB Y N 37 DND O4D C1D SING N N 38 DND C1D N1N SING N N 39 DND C6N N1N DOUB Y N 40 DND C6N C5N SING Y N 41 DND N1N C2N SING Y N 42 DND C5N C4N DOUB Y N 43 DND C2N C3N DOUB Y N 44 DND C4N C3N SING Y N 45 DND C3N C7N SING N N 46 DND C7N O7N DOUB N N 47 DND C7N O8N SING N N 48 DND O12 H1 SING N N 49 DND C5D H2 SING N N 50 DND C5D H3 SING N N 51 DND C4D H4 SING N N 52 DND C3D H5 SING N N 53 DND O3D H6 SING N N 54 DND C2D H7 SING N N 55 DND O2D H8 SING N N 56 DND C1D H9 SING N N 57 DND C6N H10 SING N N 58 DND C5N H11 SING N N 59 DND C4N H12 SING N N 60 DND C2N H13 SING N N 61 DND O8N H14 SING N N 62 DND O14 H15 SING N N 63 DND C5B H16 SING N N 64 DND C5B H17 SING N N 65 DND C4B H18 SING N N 66 DND C3B H19 SING N N 67 DND O3B H20 SING N N 68 DND C2B H21 SING N N 69 DND O2B H22 SING N N 70 DND C1B H23 SING N N 71 DND C2A H24 SING N N 72 DND C8A H25 SING N N 73 DND N6A H26 SING N N 74 DND N6A H27 SING N N 75 # # 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 DND InChI InChI 1.03 "InChI=1S/C21H26N6O15P2/c22-17-12-18(24-7-23-17)27(8-25-12)20-16(31)14(29)11(41-20)6-39-44(36,37)42-43(34,35)38-5-10-13(28)15(30)19(40-10)26-3-1-2-9(4-26)21(32)33/h1-4,7-8,10-11,13-16,19-20,28-31H,5-6H2,(H4-,22,23,24,32,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,19-,20-/m1/s1" DND InChIKey InChI 1.03 SENPVEZBRZQVST-HISDBWNOSA-O DND SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)[n+]5cccc(c5)C(O)=O)[C@@H](O)[C@H]3O" DND SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)[n+]5cccc(c5)C(O)=O)[CH](O)[CH]3O" DND SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)O" DND SMILES "OpenEye OEToolkits" 1.7.6 "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)O" # _pdbx_chem_comp_identifier.comp_id DND _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.7.6 _pdbx_chem_comp_identifier.identifier "1-[(2R,3R,4S,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]pyridin-1-ium-3-carboxylic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DND "Create component" 2001-04-16 RCSB DND "Modify descriptor" 2011-06-04 RCSB DND "Other modification" 2014-10-13 RCSB DND "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DND _pdbx_chem_comp_synonyms.name DEAMIDO-NAD+ _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##