data_NBS # _chem_comp.id NBS _chem_comp.name ;N6-BENZYL ADENOSINE-5'-DIPHOSPHATE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H21 N5 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-01-18 _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 517.324 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NBS _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 1KSW _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 NBS PB PB P 0 1 N N N -4.707 48.145 -1.934 -2.310 0.322 -6.837 PB NBS 1 NBS O4P O4P O 0 1 N N N -5.024 48.685 -3.293 -3.383 1.364 -7.433 O4P NBS 2 NBS O5P O5P O 0 1 N N N -5.808 48.284 -0.909 -1.258 -0.082 -7.987 O5P NBS 3 NBS O6P O6P O 0 1 N N N -3.972 46.826 -1.940 -3.013 -0.891 -6.362 O6P NBS 4 NBS PA PA P 0 1 N N R -3.543 50.260 -0.276 -0.476 -0.088 -5.063 PA NBS 5 NBS O1P O1P O 0 1 N N N -2.687 51.406 -0.661 -1.271 -1.401 -4.576 O1P NBS 6 NBS O2P O2P O 0 1 N N N -4.848 50.534 0.382 0.462 -0.453 -6.147 O2P NBS 7 NBS O3P O3P O 0 1 N N N -3.564 49.311 -1.621 -1.526 1.003 -5.607 O3P NBS 8 NBS "O5'" O5* O 0 1 N N N -2.610 49.421 0.740 0.347 0.529 -3.825 "O5'" NBS 9 NBS "C5'" C5* C 0 1 N N N -1.573 48.533 0.307 1.257 -0.482 -3.389 "C5'" NBS 10 NBS "C4'" C4* C 0 1 N N R -0.651 49.114 -0.784 2.076 0.043 -2.207 "C4'" NBS 11 NBS "O4'" O4* O 0 1 N N N -0.010 50.364 -0.381 1.207 0.366 -1.097 "O4'" NBS 12 NBS "C1'" C1* C 0 1 N N R 1.284 50.048 0.196 2.059 0.366 0.068 "C1'" NBS 13 NBS N9 N9 N 0 1 Y N N 1.216 50.221 1.663 1.263 0.192 1.285 N9 NBS 14 NBS C4 C4 C 0 1 Y N N 2.281 50.338 2.523 1.607 0.605 2.547 C4 NBS 15 NBS N3 N3 N 0 1 Y N N 3.589 50.268 2.200 2.646 1.246 3.073 N3 NBS 16 NBS C2 C2 C 0 1 Y N N 4.356 50.437 3.278 2.685 1.515 4.362 C2 NBS 17 NBS N1 N1 N 0 1 Y N N 3.983 50.648 4.538 1.712 1.174 5.187 N1 NBS 18 NBS C6 C6 C 0 1 Y N N 2.667 50.715 4.839 0.632 0.535 4.751 C6 NBS 19 NBS N6 N6 N 0 1 N N N 2.300 50.986 6.161 -0.382 0.182 5.623 N6 NBS 20 NBS CB1 CB1 C 0 1 N N N 0.977 50.744 6.712 -0.272 0.513 7.046 CB1 NBS 21 NBS CB2 CB2 C 0 1 Y N N 0.074 52.009 6.767 -1.498 0.022 7.772 CB2 NBS 22 NBS CB3 CB3 C 0 1 Y N N -0.834 52.160 7.806 -1.521 -1.251 8.307 CB3 NBS 23 NBS CB4 CB4 C 0 1 Y N N -1.704 53.277 7.856 -2.646 -1.701 8.973 CB4 NBS 24 NBS CB5 CB5 C 0 1 Y N N -1.641 54.242 6.839 -3.748 -0.877 9.104 CB5 NBS 25 NBS CB6 CB6 C 0 1 Y N N -0.724 54.091 5.798 -3.724 0.397 8.570 CB6 NBS 26 NBS CB7 CB7 C 0 1 Y N N 0.139 52.966 5.774 -2.598 0.849 7.908 CB7 NBS 27 NBS C5 C5 C 0 1 Y N N 1.754 50.560 3.772 0.543 0.226 3.383 C5 NBS 28 NBS N7 N7 N 0 1 Y N N 0.370 50.566 3.712 -0.374 -0.394 2.604 N7 NBS 29 NBS C8 C8 C 0 1 Y N N 0.107 50.359 2.457 0.046 -0.415 1.372 C8 NBS 30 NBS "C2'" C2* C 0 1 N N R 1.602 48.606 -0.167 3.003 -0.839 -0.133 "C2'" NBS 31 NBS "O2'" O2* O 0 1 N N N 2.850 48.522 -0.850 4.317 -0.535 0.339 "O2'" NBS 32 NBS "C3'" C3* C 0 1 N N S 0.470 48.143 -1.051 3.015 -1.055 -1.663 "C3'" NBS 33 NBS "O3'" O3* O 0 1 N N N 0.810 48.231 -2.417 4.336 -0.887 -2.182 "O3'" NBS 34 NBS HOP4 4HOP H 0 0 N N N -4.331 48.597 -3.937 -3.829 0.917 -8.165 HOP4 NBS 35 NBS HOP5 5HOP H 0 0 N N N -5.606 47.941 -0.046 -0.823 0.734 -8.267 HOP5 NBS 36 NBS HOP1 1HOP H 0 0 N N N -1.853 51.230 -1.081 -1.870 -1.120 -3.871 HOP1 NBS 37 NBS "H5'1" 1H5* H 0 0 N N N -0.971 48.183 1.178 1.928 -0.745 -4.207 "H5'1" NBS 38 NBS "H5'2" 2H5* H 0 0 N N N -2.007 47.562 -0.027 0.698 -1.365 -3.079 "H5'2" NBS 39 NBS "H4'" H4* H 0 1 N N N -1.296 49.297 -1.674 2.652 0.919 -2.506 "H4'" NBS 40 NBS "H1'" H1* H 0 1 N N N 2.082 50.721 -0.194 2.632 1.292 0.119 "H1'" NBS 41 NBS H2 H2 H 0 1 N N N 5.444 50.396 3.104 3.546 2.033 4.758 H2 NBS 42 NBS H6 H6 H 0 1 N N N 2.519 51.966 6.335 -1.165 -0.283 5.293 H6 NBS 43 NBS HB11 1HB1 H 0 0 N N N 0.466 49.922 6.157 0.613 0.033 7.463 HB11 NBS 44 NBS HB12 2HB1 H 0 0 N N N 1.052 50.272 7.719 -0.189 1.593 7.163 HB12 NBS 45 NBS HB3 HB3 H 0 1 N N N -0.864 51.389 8.594 -0.660 -1.896 8.205 HB3 NBS 46 NBS HB4 HB4 H 0 1 N N N -2.425 53.394 8.681 -2.664 -2.697 9.390 HB4 NBS 47 NBS HB5 HB5 H 0 1 N N N -2.311 55.117 6.857 -4.627 -1.228 9.623 HB5 NBS 48 NBS HB6 HB6 H 0 1 N N N -0.681 54.853 5.002 -4.585 1.041 8.672 HB6 NBS 49 NBS HB7 HB7 H 0 1 N N N 0.877 52.832 4.965 -2.580 1.845 7.490 HB7 NBS 50 NBS H8 H8 H 0 1 N N N -0.937 50.306 2.106 -0.490 -0.851 0.542 H8 NBS 51 NBS "H2'" H2* H 0 1 N N N 1.693 47.965 0.741 2.611 -1.721 0.373 "H2'" NBS 52 NBS "HO'2" 2HO* H 0 0 N N N 3.048 47.621 -1.076 4.873 -1.299 0.131 "HO'2" NBS 53 NBS "H3'" H3* H 0 1 N N N 0.210 47.080 -0.835 2.630 -2.044 -1.912 "H3'" NBS 54 NBS "HO'3" 3HO* H 0 0 N N N 1.516 47.618 -2.585 4.882 -1.580 -1.786 "HO'3" NBS 55 # 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 NBS PB O4P SING N N 1 NBS PB O5P SING N N 2 NBS PB O6P DOUB N N 3 NBS PB O3P SING N N 4 NBS O4P HOP4 SING N N 5 NBS O5P HOP5 SING N N 6 NBS PA O1P SING N N 7 NBS PA O2P DOUB N N 8 NBS PA O3P SING N N 9 NBS PA "O5'" SING N N 10 NBS O1P HOP1 SING N N 11 NBS "O5'" "C5'" SING N N 12 NBS "C5'" "C4'" SING N N 13 NBS "C5'" "H5'1" SING N N 14 NBS "C5'" "H5'2" SING N N 15 NBS "C4'" "O4'" SING N N 16 NBS "C4'" "C3'" SING N N 17 NBS "C4'" "H4'" SING N N 18 NBS "O4'" "C1'" SING N N 19 NBS "C1'" N9 SING N N 20 NBS "C1'" "C2'" SING N N 21 NBS "C1'" "H1'" SING N N 22 NBS N9 C4 SING Y N 23 NBS N9 C8 SING Y N 24 NBS C4 N3 DOUB Y N 25 NBS C4 C5 SING Y N 26 NBS N3 C2 SING Y N 27 NBS C2 N1 DOUB Y N 28 NBS C2 H2 SING N N 29 NBS N1 C6 SING Y N 30 NBS C6 N6 SING N N 31 NBS C6 C5 DOUB Y N 32 NBS N6 CB1 SING N N 33 NBS N6 H6 SING N N 34 NBS CB1 CB2 SING N N 35 NBS CB1 HB11 SING N N 36 NBS CB1 HB12 SING N N 37 NBS CB2 CB3 DOUB Y N 38 NBS CB2 CB7 SING Y N 39 NBS CB3 CB4 SING Y N 40 NBS CB3 HB3 SING N N 41 NBS CB4 CB5 DOUB Y N 42 NBS CB4 HB4 SING N N 43 NBS CB5 CB6 SING Y N 44 NBS CB5 HB5 SING N N 45 NBS CB6 CB7 DOUB Y N 46 NBS CB6 HB6 SING N N 47 NBS CB7 HB7 SING N N 48 NBS C5 N7 SING Y N 49 NBS N7 C8 DOUB Y N 50 NBS C8 H8 SING N N 51 NBS "C2'" "O2'" SING N N 52 NBS "C2'" "C3'" SING N N 53 NBS "C2'" "H2'" SING N N 54 NBS "O2'" "HO'2" SING N N 55 NBS "C3'" "O3'" SING N N 56 NBS "C3'" "H3'" SING N N 57 NBS "O3'" "HO'3" SING N N 58 # 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 NBS SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC4OC(n2cnc1c(ncnc12)NCc3ccccc3)C(O)C4O" NBS SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P](O)(O)=O)n2cnc3c(NCc4ccccc4)ncnc23" NBS SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3c(NCc4ccccc4)ncnc23" NBS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)CNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO[P@@](=O)(O)OP(=O)(O)O)O)O" NBS SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)CNc2c3c(ncn2)n(cn3)C4C(C(C(O4)COP(=O)(O)OP(=O)(O)O)O)O" NBS InChI InChI 1.03 "InChI=1S/C17H21N5O10P2/c23-13-11(7-30-34(28,29)32-33(25,26)27)31-17(14(13)24)22-9-21-12-15(19-8-20-16(12)22)18-6-10-4-2-1-3-5-10/h1-5,8-9,11,13-14,17,23-24H,6-7H2,(H,28,29)(H,18,19,20)(H2,25,26,27)/t11-,13-,14-,17-/m1/s1" NBS InChIKey InChI 1.03 MRHGMAGSDAQUFH-LSCFUAHRSA-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 NBS "SYSTEMATIC NAME" ACDLabs 10.04 ;N-benzyladenosine 5'-(trihydrogen diphosphate) ; NBS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(phenylmethylamino)purin-9-yl]oxolan-2-yl]methyl phosphono hydrogen 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 NBS "Create component" 2002-01-18 RCSB NBS "Modify descriptor" 2011-06-04 RCSB #