data_PAD # _chem_comp.id PAD _chem_comp.name "5-BETA-D-RIBOFURANOSYLPICOLINAMIDE ADENINE-DINUCLEOTIDE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H27 N7 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms CPAD _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 663.425 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PAD _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 1A72 _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 PAD PA AP P 0 1 N N S 13.285 7.278 26.710 0.936 1.161 -2.186 PA PAD 1 PAD O1A AO1 O 0 1 N N N 12.092 6.356 26.757 1.558 0.572 -3.393 O1A PAD 2 PAD O2A AO2 O 0 1 N N N 14.427 6.880 25.824 0.250 2.566 -2.567 O2A PAD 3 PAD O5B AO5* O 0 1 N N N 13.973 7.599 28.159 2.066 1.401 -1.064 O5B PAD 4 PAD C5B AC5* C 0 1 N N N 13.798 6.758 29.321 3.250 2.164 -1.303 C5B PAD 5 PAD C4B AC4* C 0 1 N N R 15.143 6.947 30.016 4.103 2.194 -0.034 C4B PAD 6 PAD O4B AO4* O 0 1 N N N 15.122 6.442 31.381 4.594 0.874 0.256 O4B PAD 7 PAD C3B AC3* C 0 1 N N S 16.272 6.282 29.222 5.329 3.102 -0.247 C3B PAD 8 PAD O3B AO3* O 0 1 N N N 17.474 7.060 29.263 5.323 4.179 0.692 O3B PAD 9 PAD C2B AC2* C 0 1 N N R 16.543 5.072 30.073 6.540 2.171 0.004 C2B PAD 10 PAD O2B AO2* O 0 1 N N N 17.951 4.803 29.997 7.556 2.845 0.749 O2B PAD 11 PAD C1B AC1* C 0 1 N N R 16.220 5.545 31.475 5.905 1.031 0.841 C1B PAD 12 PAD N9A AN9 N 0 1 Y N N 15.980 4.466 32.439 6.681 -0.203 0.705 N9A PAD 13 PAD C8A AC8 C 0 1 Y N N 15.424 3.252 32.222 6.489 -1.179 -0.227 C8A PAD 14 PAD N7A AN7 N 0 1 Y N N 15.314 2.590 33.377 7.357 -2.133 -0.058 N7A PAD 15 PAD C5A AC5 C 0 1 Y N N 15.812 3.437 34.282 8.160 -1.832 0.990 C5A PAD 16 PAD C6A AC6 C 0 1 Y N N 15.892 3.178 35.639 9.245 -2.467 1.620 C6A PAD 17 PAD N6A AN6 N 0 1 N N N 15.670 1.973 36.124 9.707 -3.691 1.169 N6A PAD 18 PAD N1A AN1 N 0 1 Y N N 16.423 4.158 36.379 9.816 -1.864 2.657 N1A PAD 19 PAD C2A AC2 C 0 1 Y N N 16.847 5.299 35.818 9.382 -0.696 3.094 C2A PAD 20 PAD N3A AN3 N 0 1 Y N N 16.791 5.552 34.513 8.370 -0.065 2.536 N3A PAD 21 PAD C4A AC4 C 0 1 Y N N 16.252 4.615 33.722 7.740 -0.587 1.489 C4A PAD 22 PAD O3 O3 O 0 1 N N N 12.915 8.845 26.498 -0.183 0.155 -1.613 O3 PAD 23 PAD PN NP P 0 1 N N N 11.655 9.733 27.031 -1.298 -0.785 -2.297 PN PAD 24 PAD O1N NO1 O 0 1 N N N 11.350 10.824 26.043 -1.937 -0.040 -3.490 O1N PAD 25 PAD O2N NO2 O -1 1 N N N 12.034 10.231 28.406 -0.636 -2.088 -2.799 O2N PAD 26 PAD O5D NO5* O 0 1 N N N 10.562 8.517 27.031 -2.435 -1.142 -1.216 O5D PAD 27 PAD C5D NC5* C 0 1 N N N 10.486 7.881 28.328 -3.617 -1.875 -1.543 C5D PAD 28 PAD C4D NC4* C 0 1 N N R 9.299 8.379 29.103 -4.480 -2.038 -0.289 C4D PAD 29 PAD O4D NO4* O 0 1 N N N 9.167 9.802 29.263 -4.984 -0.759 0.150 O4D PAD 30 PAD C3D NC3* C 0 1 N N S 8.192 7.851 28.250 -5.765 -2.842 -0.612 C3D PAD 31 PAD O3D NO3* O 0 1 N N N 8.169 6.429 28.339 -5.526 -4.247 -0.510 O3D PAD 32 PAD C2D NC2* C 0 1 N N R 7.030 8.655 28.789 -6.733 -2.365 0.497 C2D PAD 33 PAD O2D NO2* O 0 1 N N N 6.522 7.937 29.921 -6.758 -3.301 1.576 O2D PAD 34 PAD C1D NC1* C 0 1 N N S 7.738 9.951 29.156 -6.140 -1.021 0.963 C1D PAD 35 PAD C1N NC1 C 0 1 Y N N 7.586 10.768 27.940 -7.155 0.078 0.780 C1N PAD 36 PAD N2N NN2 N 1 1 Y N N 8.294 10.427 26.762 -7.913 0.437 1.793 N2N PAD 37 PAD C3N NC3 C 0 1 Y N N 8.211 11.249 25.634 -8.820 1.399 1.678 C3N PAD 38 PAD C7N NC7 C 0 1 N N N 8.919 10.877 24.328 -9.651 1.769 2.848 C7N PAD 39 PAD O7N NO7 O 0 1 N N N 9.224 11.807 23.576 -10.483 2.649 2.749 O7N PAD 40 PAD N7N NN7 N 0 1 N N N 9.165 9.575 24.075 -9.484 1.129 4.023 N7N PAD 41 PAD C4N NC4 C 0 1 Y N N 7.462 12.423 25.679 -8.997 2.064 0.468 C4N PAD 42 PAD C5N NC5 C 0 1 Y N N 6.752 12.741 26.853 -8.212 1.707 -0.618 C5N PAD 43 PAD C6N NC6 C 0 1 Y N N 6.806 11.915 27.976 -7.273 0.701 -0.452 C6N PAD 44 PAD HOA2 2HOA H 0 0 N N N 15.178 7.460 25.794 -0.178 3.010 -1.822 HOA2 PAD 45 PAD H51A AH51 H 0 0 N N N 12.900 6.979 29.943 3.819 1.708 -2.113 H51A PAD 46 PAD H52A AH52 H 0 0 N N N 13.510 5.701 29.110 2.976 3.182 -1.581 H52A PAD 47 PAD H4B AH4* H 0 1 N N N 15.335 8.044 30.059 3.509 2.560 0.803 H4B PAD 48 PAD H3B AH3* H 0 1 N N N 16.000 6.116 28.153 5.346 3.487 -1.267 H3B PAD 49 PAD HO3A AHO3 H 0 0 N N N 18.174 6.647 28.770 6.074 4.783 0.603 HO3A PAD 50 PAD H2B AH2* H 0 1 N N N 15.969 4.164 29.773 6.938 1.788 -0.936 H2B PAD 51 PAD HO2A AHO2 H 0 0 N N N 18.122 4.038 30.534 7.921 3.621 0.303 HO2A PAD 52 PAD H1B AH1* H 0 1 N N N 17.116 6.061 31.889 5.825 1.322 1.888 H1B PAD 53 PAD H8A AH8 H 0 1 N N N 15.105 2.857 31.242 5.727 -1.163 -0.993 H8A PAD 54 PAD H61A AH61 H 0 0 N N N 15.729 1.782 37.124 9.282 -4.120 0.410 H61A PAD 55 PAD H62A AH62 H 0 0 N N N 16.290 1.321 35.643 10.456 -4.119 1.612 H62A PAD 56 PAD H2A AH2 H 0 1 N N N 17.269 6.080 36.472 9.875 -0.241 3.940 H2A PAD 57 PAD H51N NH51 H 0 0 N N N 10.483 6.769 28.241 -4.181 -1.335 -2.304 H51N PAD 58 PAD H52N NH52 H 0 0 N N N 11.433 8.004 28.902 -3.341 -2.858 -1.924 H52N PAD 59 PAD H4D NH4* H 0 1 N N N 9.345 8.046 30.166 -3.911 -2.521 0.506 H4D PAD 60 PAD H3D NH3* H 0 1 N N N 8.240 7.977 27.143 -6.147 -2.585 -1.600 H3D PAD 61 PAD HO3N NHO3 H 0 0 N N N 7.465 6.093 27.796 -6.301 -4.793 -0.703 HO3N PAD 62 PAD H2D NH2* H 0 1 N N N 6.156 8.834 28.119 -7.735 -2.222 0.094 H2D PAD 63 PAD HO2N NHO2 H 0 0 N N N 5.792 8.442 30.259 -7.068 -4.182 1.326 HO2N PAD 64 PAD H1D NH1* H 0 1 N N N 7.327 10.338 30.117 -5.849 -1.088 2.011 H1D PAD 65 PAD H2N NH2 H 0 1 N N N 8.867 9.584 26.725 -7.806 -0.014 2.646 H2N PAD 66 PAD H71N NH71 H 0 0 N N N 8.912 8.806 24.696 -8.820 0.426 4.102 H71N PAD 67 PAD H72N NH72 H 0 0 N N N 9.636 9.327 23.205 -10.028 1.371 4.788 H72N PAD 68 PAD H4N NH4 H 0 1 N N N 7.431 13.089 24.800 -9.735 2.847 0.376 H4N PAD 69 PAD H5N NH5 H 0 1 N N N 6.139 13.657 26.893 -8.326 2.205 -1.569 H5N PAD 70 PAD H6N NH6 H 0 1 N N N 6.236 12.167 28.886 -6.644 0.402 -1.277 H6N PAD 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 PAD PA O1A DOUB N N 1 PAD PA O2A SING N N 2 PAD PA O5B SING N N 3 PAD PA O3 SING N N 4 PAD O2A HOA2 SING N N 5 PAD O5B C5B SING N N 6 PAD C5B C4B SING N N 7 PAD C5B H51A SING N N 8 PAD C5B H52A SING N N 9 PAD C4B O4B SING N N 10 PAD C4B C3B SING N N 11 PAD C4B H4B SING N N 12 PAD O4B C1B SING N N 13 PAD C3B O3B SING N N 14 PAD C3B C2B SING N N 15 PAD C3B H3B SING N N 16 PAD O3B HO3A SING N N 17 PAD C2B O2B SING N N 18 PAD C2B C1B SING N N 19 PAD C2B H2B SING N N 20 PAD O2B HO2A SING N N 21 PAD C1B N9A SING N N 22 PAD C1B H1B SING N N 23 PAD N9A C8A SING Y N 24 PAD N9A C4A SING Y N 25 PAD C8A N7A DOUB Y N 26 PAD C8A H8A SING N N 27 PAD N7A C5A SING Y N 28 PAD C5A C6A SING Y N 29 PAD C5A C4A DOUB Y N 30 PAD C6A N6A SING N N 31 PAD C6A N1A DOUB Y N 32 PAD N6A H61A SING N N 33 PAD N6A H62A SING N N 34 PAD N1A C2A SING Y N 35 PAD C2A N3A DOUB Y N 36 PAD C2A H2A SING N N 37 PAD N3A C4A SING Y N 38 PAD O3 PN SING N N 39 PAD PN O1N DOUB N N 40 PAD PN O2N SING N N 41 PAD PN O5D SING N N 42 PAD O5D C5D SING N N 43 PAD C5D C4D SING N N 44 PAD C5D H51N SING N N 45 PAD C5D H52N SING N N 46 PAD C4D O4D SING N N 47 PAD C4D C3D SING N N 48 PAD C4D H4D SING N N 49 PAD O4D C1D SING N N 50 PAD C3D O3D SING N N 51 PAD C3D C2D SING N N 52 PAD C3D H3D SING N N 53 PAD O3D HO3N SING N N 54 PAD C2D O2D SING N N 55 PAD C2D C1D SING N N 56 PAD C2D H2D SING N N 57 PAD O2D HO2N SING N N 58 PAD C1D C1N SING N N 59 PAD C1D H1D SING N N 60 PAD C1N N2N DOUB Y N 61 PAD C1N C6N SING Y N 62 PAD N2N C3N SING Y N 63 PAD N2N H2N SING N N 64 PAD C3N C7N SING N N 65 PAD C3N C4N DOUB Y N 66 PAD C7N O7N DOUB N N 67 PAD C7N N7N SING N N 68 PAD N7N H71N SING N N 69 PAD N7N H72N SING N N 70 PAD C4N C5N SING Y N 71 PAD C4N H4N SING N N 72 PAD C5N C6N DOUB Y N 73 PAD C5N H5N SING N N 74 PAD C6N H6N 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 PAD InChI InChI 1.03 "InChI=1S/C21H27N7O14P2/c22-18-12-20(25-6-24-18)28(7-26-12)21-16(32)14(30)11(41-21)5-39-44(36,37)42-43(34,35)38-4-10-13(29)15(31)17(40-10)8-2-1-3-9(27-8)19(23)33/h1-3,6-7,10-11,13-17,21,29-32H,4-5H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,17+,21-/m1/s1" PAD InChIKey InChI 1.03 LFERELMXERXKKQ-KMXXXSRASA-N PAD SMILES_CANONICAL CACTVS 3.385 "NC(=O)c1cccc([nH+]1)[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" PAD SMILES CACTVS 3.385 "NC(=O)c1cccc([nH+]1)[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" PAD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "c1cc([nH+]c(c1)C(=O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O" PAD SMILES "OpenEye OEToolkits" 1.7.5 "c1cc([nH+]c(c1)C(=O)N)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id PAD _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,5S)-5-(6-aminocarbonylpyridin-1-ium-2-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 PAD "Create component" 1999-07-08 RCSB PAD "Modify descriptor" 2011-06-04 RCSB PAD "Modify descriptor" 2012-01-05 RCSB PAD "Modify coordinates" 2012-01-05 RCSB PAD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PAD _pdbx_chem_comp_synonyms.name CPAD _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##