data_SND # _chem_comp.id SND _chem_comp.name THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H27 N7 O13 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-04-26 _chem_comp.pdbx_modified_date 2012-01-05 _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 679.491 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SND _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 1PTJ _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 SND PA AP P 0 1 N N S -7.484 5.957 26.950 1.168 -0.151 -2.482 PA SND 1 SND O1A AO1 O 0 1 N N N -7.217 4.557 27.370 1.826 -1.232 -3.249 O1A SND 2 SND O2A AO2 O 0 1 N N N -7.007 6.927 27.971 0.460 0.875 -3.501 O2A SND 3 SND O5B AO5* O 0 1 N N N -9.043 6.167 26.669 2.269 0.635 -1.609 O5B SND 4 SND C5B AC5* C 0 1 N N N -10.013 5.112 26.838 3.441 1.220 -2.178 C5B SND 5 SND C4B AC4* C 0 1 N N R -11.287 5.496 26.123 4.267 1.884 -1.074 C4B SND 6 SND O4B AO4* O 0 1 N N N -12.070 6.289 27.051 4.780 0.883 -0.178 O4B SND 7 SND C3B AC3* C 0 1 N N S -11.178 6.428 24.890 5.479 2.610 -1.691 C3B SND 8 SND O3B AO3* O 0 1 N N N -11.560 5.899 23.645 5.431 4.006 -1.391 O3B SND 9 SND C2B AC2* C 0 1 N N R -11.975 7.658 25.309 6.703 1.951 -1.011 C2B SND 10 SND O2B AO2* O 0 1 N N N -12.467 8.455 24.259 7.689 2.929 -0.678 O2B SND 11 SND C1B AC1* C 0 1 N N R -12.992 6.985 26.222 6.075 1.340 0.268 C1B SND 12 SND N9A AN9 N 0 1 Y N N -13.785 7.851 27.145 6.880 0.216 0.752 N9A SND 13 SND C8A AC8 C 0 1 Y N N -13.334 8.782 28.065 6.727 -1.093 0.407 C8A SND 14 SND N7A AN7 N 0 1 Y N N -14.319 9.390 28.750 7.611 -1.822 1.024 N7A SND 15 SND C5A AC5 C 0 1 Y N N -15.464 8.819 28.242 8.386 -1.028 1.801 C5A SND 16 SND C6A AC6 C 0 1 Y N N -16.860 9.010 28.532 9.470 -1.248 2.668 C6A SND 17 SND N6A AN6 N 0 1 N N N -17.319 9.868 29.442 9.967 -2.524 2.870 N6A SND 18 SND N1A AN1 N 0 1 Y N N -17.794 8.236 27.804 10.008 -0.204 3.289 N1A SND 19 SND C2A AC2 C 0 1 Y N N -17.349 7.320 26.839 9.540 1.018 3.102 C2A SND 20 SND N3A AN3 N 0 1 Y N N -16.075 7.088 26.517 8.527 1.271 2.301 N3A SND 21 SND C4A AC4 C 0 1 Y N N -15.162 7.862 27.245 7.930 0.290 1.632 C4A SND 22 SND O3 O3 O 0 1 N N N -7.082 6.245 25.463 0.058 -0.785 -1.503 O3 SND 23 SND PN NP P 0 1 N N N -6.458 5.296 24.441 -1.022 -1.969 -1.655 PN SND 24 SND O1N NO1 O 0 1 N N N -7.317 4.096 24.265 -1.653 -1.913 -3.065 O1N SND 25 SND O2N NO2 O -1 1 N N N -5.124 4.868 24.922 -0.323 -3.333 -1.458 O2N SND 26 SND O5D NO5* O 0 1 N N N -6.319 6.029 23.147 -2.174 -1.791 -0.545 O5D SND 27 SND C5D NC5* C 0 1 N N N -7.330 6.369 22.257 -3.334 -2.623 -0.485 C5D SND 28 SND C4D NC4* C 0 1 N N R -7.194 6.991 21.148 -4.218 -2.184 0.684 C4D SND 29 SND O4D NO4* O 0 1 N N N -5.853 7.578 21.157 -4.747 -0.872 0.430 O4D SND 30 SND C3D NC3* C 0 1 N N S -7.268 5.940 20.028 -5.417 -3.142 0.823 C3D SND 31 SND O3D NO3* O 0 1 N N N -8.167 6.413 19.016 -5.410 -3.769 2.107 O3D SND 32 SND C2D NC2* C 0 1 N N R -5.802 5.780 19.574 -6.655 -2.224 0.674 C2D SND 33 SND O2D NO2* O 0 1 N N N -5.617 5.711 18.464 -7.674 -2.588 1.608 O2D SND 34 SND C1D NC1* C 0 1 N N R -5.047 6.994 20.104 -6.068 -0.830 1.011 C1D SND 35 SND N1N NN1 N 1 1 Y N N -3.716 6.716 20.575 -6.869 0.230 0.394 N1N SND 36 SND C2N NC2 C 0 1 Y N N -2.665 7.299 19.848 -7.682 0.939 1.150 C2N SND 37 SND C3N NC3 C 0 1 Y N N -1.341 7.060 20.263 -8.460 1.956 0.594 C3N SND 38 SND C7N NC7 C 0 1 N N N -0.010 7.597 19.613 -9.371 2.751 1.441 C7N SND 39 SND S7N NS7 S 0 1 N N N -0.178 8.504 18.285 -8.931 3.130 3.052 S7N SND 40 SND N7N NN7 N 0 1 N N N 1.231 7.186 19.932 -10.550 3.180 0.946 N7N SND 41 SND C4N NC4 C 0 1 Y N N -1.050 6.220 21.430 -8.362 2.209 -0.780 C4N SND 42 SND C5N NC5 C 0 1 Y N N -2.164 5.665 22.114 -7.493 1.436 -1.528 C5N SND 43 SND C6N NC6 C 0 1 Y N N -3.504 5.849 21.774 -6.753 0.450 -0.902 C6N SND 44 SND HOA2 2HOA H 0 0 N N N -6.905 6.485 28.806 0.008 1.612 -3.068 HOA2 SND 45 SND H51A AH51 H 0 0 N N N -9.619 4.176 26.414 4.037 0.444 -2.661 H51A SND 46 SND H52A AH52 H 0 0 N N N -10.218 4.964 27.909 3.152 1.968 -2.916 H52A SND 47 SND H4B AH4* H 0 1 N N N -11.690 4.532 25.781 3.649 2.592 -0.524 H4B SND 48 SND H3B AH3* H 0 1 N N N -10.122 6.637 24.664 5.509 2.453 -2.770 H3B SND 49 SND HO3A AHO3 H 0 0 N N N -11.646 6.604 23.014 6.170 4.512 -1.755 HO3A SND 50 SND H2B AH2* H 0 1 N N N -11.398 8.454 25.801 7.128 1.173 -1.645 H2B SND 51 SND HO2A AHO2 H 0 0 N N N -12.578 9.348 24.564 8.047 3.403 -1.441 HO2A SND 52 SND H1B AH1* H 0 1 N N N -13.761 6.464 25.633 5.968 2.100 1.042 H1B SND 53 SND H8A AH8 H 0 1 N N N -12.287 9.000 28.219 5.981 -1.471 -0.277 H8A SND 54 SND H61A AH61 H 0 0 N N N -17.434 9.397 30.317 9.567 -3.279 2.411 H61A SND 55 SND H62A AH62 H 0 0 N N N -16.667 10.619 29.551 10.716 -2.664 3.471 H62A SND 56 SND H2A AH2 H 0 1 N N N -18.102 6.754 26.311 10.007 1.839 3.626 H2A SND 57 SND H51N NH51 H 0 0 N N N -7.770 5.403 21.970 -3.892 -2.535 -1.417 H51N SND 58 SND H52N NH52 H 0 0 N N N -7.853 7.137 22.845 -3.029 -3.660 -0.341 H52N SND 59 SND H4D NH4* H 0 1 N N N -7.961 7.766 21.002 -3.637 -2.178 1.606 H4D SND 60 SND H3D NH3* H 0 1 N N N -7.669 4.958 20.321 -5.399 -3.893 0.033 H3D SND 61 SND HO3N NHO3 H 0 0 N N N -9.035 6.518 19.387 -6.143 -4.383 2.249 HO3N SND 62 SND H2D NH2* H 0 1 N N N -5.466 4.810 19.970 -7.038 -2.250 -0.346 H2D SND 63 SND HO2N NHO2 H 0 0 N N N -6.448 5.692 18.005 -8.009 -3.488 1.494 HO2N SND 64 SND H1D NH1* H 0 1 N N N -4.897 7.690 19.266 -6.008 -0.689 2.090 H1D SND 65 SND H2N NH2 H 0 1 N N N -2.869 7.919 18.987 -7.746 0.732 2.208 H2N SND 66 SND H71N NH71 H 0 0 N N N 1.098 6.583 20.719 -10.799 2.965 0.034 H71N SND 67 SND H72N NH72 H 0 0 N N N 2.091 7.429 19.484 -11.148 3.702 1.503 H72N SND 68 SND H4N NH4 H 0 1 N N N -0.037 6.033 21.754 -8.950 2.988 -1.243 H4N SND 69 SND H5N NH5 H 0 1 N N N -1.955 5.046 22.974 -7.392 1.602 -2.591 H5N SND 70 SND H6N NH6 H 0 1 N N N -4.317 5.404 22.328 -6.071 -0.153 -1.483 H6N SND 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 SND PA O1A DOUB N N 1 SND PA O2A SING N N 2 SND PA O5B SING N N 3 SND PA O3 SING N N 4 SND O2A HOA2 SING N N 5 SND O5B C5B SING N N 6 SND C5B C4B SING N N 7 SND C5B H51A SING N N 8 SND C5B H52A SING N N 9 SND C4B O4B SING N N 10 SND C4B C3B SING N N 11 SND C4B H4B SING N N 12 SND O4B C1B SING N N 13 SND C3B O3B SING N N 14 SND C3B C2B SING N N 15 SND C3B H3B SING N N 16 SND O3B HO3A SING N N 17 SND C2B O2B SING N N 18 SND C2B C1B SING N N 19 SND C2B H2B SING N N 20 SND O2B HO2A SING N N 21 SND C1B N9A SING N N 22 SND C1B H1B SING N N 23 SND N9A C8A SING Y N 24 SND N9A C4A SING Y N 25 SND C8A N7A DOUB Y N 26 SND C8A H8A SING N N 27 SND N7A C5A SING Y N 28 SND C5A C6A SING Y N 29 SND C5A C4A DOUB Y N 30 SND C6A N6A SING N N 31 SND C6A N1A DOUB Y N 32 SND N6A H61A SING N N 33 SND N6A H62A SING N N 34 SND N1A C2A SING Y N 35 SND C2A N3A DOUB Y N 36 SND C2A H2A SING N N 37 SND N3A C4A SING Y N 38 SND O3 PN SING N N 39 SND PN O1N DOUB N N 40 SND PN O2N SING N N 41 SND PN O5D SING N N 42 SND O5D C5D SING N N 43 SND C5D C4D SING N N 44 SND C5D H51N SING N N 45 SND C5D H52N SING N N 46 SND C4D O4D SING N N 47 SND C4D C3D SING N N 48 SND C4D H4D SING N N 49 SND O4D C1D SING N N 50 SND C3D O3D SING N N 51 SND C3D C2D SING N N 52 SND C3D H3D SING N N 53 SND O3D HO3N SING N N 54 SND C2D O2D SING N N 55 SND C2D C1D SING N N 56 SND C2D H2D SING N N 57 SND O2D HO2N SING N N 58 SND C1D N1N SING N N 59 SND C1D H1D SING N N 60 SND N1N C2N DOUB Y N 61 SND N1N C6N SING Y N 62 SND C2N C3N SING Y N 63 SND C2N H2N SING N N 64 SND C3N C7N SING N N 65 SND C3N C4N DOUB Y N 66 SND C7N S7N DOUB N N 67 SND C7N N7N SING N N 68 SND N7N H71N SING N N 69 SND N7N H72N SING N N 70 SND C4N C5N SING Y N 71 SND C4N H4N SING N N 72 SND C5N C6N DOUB Y N 73 SND C5N H5N SING N N 74 SND 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 SND InChI InChI 1.03 ;InChI=1S/C21H27N7O13P2S/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(40-21)6-38-43(35,36)41-42(33,34)37-5-10-13(29)15(31)20(39-10)27-3-1-2-9(4-27)18(23)44/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,44)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 ; SND InChIKey InChI 1.03 UQYPZLRUJKCREN-NNYOXOHSSA-N SND SMILES_CANONICAL CACTVS 3.385 "NC(=S)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(N)ncnc45)[C@@H](O)[C@H]2O" SND SMILES CACTVS 3.385 "NC(=S)c1ccc[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" SND SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "c1cc(c[n+](c1)[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)C(=S)N" SND SMILES "OpenEye OEToolkits" 1.7.5 "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=S)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 SND "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(3-carbamothioylpyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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 SND "Create component" 2001-04-26 RCSB SND "Modify descriptor" 2011-06-04 RCSB SND "Modify descriptor" 2012-01-05 RCSB SND "Modify coordinates" 2012-01-05 RCSB #