data_1RB # _chem_comp.id 1RB _chem_comp.name "1-ALPHA-D-RIBOFURANOSYL-BENZIMIAZOLE-5'-PHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H15 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "ALPHA-RIBAZOLE-5'-PHOSPHATE DERIVATIVE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-03-19 _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 330.230 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1RB _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 1L5K _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 1RB N3 N3 N 0 1 Y N N 56.347 41.611 14.094 2.444 -1.847 1.096 N3 1RB 1 1RB N1 N1 N 0 1 Y N N 56.621 40.906 11.923 1.870 -0.308 -0.340 N1 1RB 2 1RB C2 C2 C 0 1 Y N N 55.848 40.934 13.053 1.433 -1.222 0.568 C2 1RB 3 1RB C7A C7A C 0 1 Y N N 57.762 41.669 12.327 3.248 -0.387 -0.372 C7A 1RB 4 1RB C3A C3A C 0 1 Y N N 57.564 42.105 13.693 3.601 -1.377 0.562 C3A 1RB 5 1RB C4 C4 C 0 1 Y N N 58.538 42.896 14.369 4.949 -1.685 0.761 C4 1RB 6 1RB C5 C5 C 0 1 Y N N 59.714 43.259 13.687 5.911 -1.020 0.053 C5 1RB 7 1RB C6 C6 C 0 1 Y N N 59.933 42.839 12.324 5.563 -0.039 -0.864 C6 1RB 8 1RB C7 C7 C 0 1 Y N N 58.968 42.052 11.643 4.239 0.281 -1.076 C7 1RB 9 1RB P P P 0 1 N N N 59.270 39.315 6.026 -4.523 -0.564 -0.112 P 1RB 10 1RB O1P O1P O 0 1 N N N 59.049 38.066 5.233 -4.909 0.385 -1.180 O1P 1RB 11 1RB O2P O2P O 0 1 N N N 59.548 40.466 5.115 -5.171 -2.006 -0.415 O2P 1RB 12 1RB O3P O3P O 0 1 N N N 60.434 39.125 6.952 -5.060 -0.022 1.306 O3P 1RB 13 1RB "O5'" O5* O 0 1 N N N 57.956 39.641 6.898 -2.919 -0.695 -0.064 "O5'" 1RB 14 1RB "C5'" C5* C 0 1 N N N 57.469 38.691 7.845 -2.401 0.628 0.090 "C5'" 1RB 15 1RB "C4'" C4* C 0 1 N N R 57.951 39.095 9.241 -0.873 0.574 0.143 "C4'" 1RB 16 1RB "O4'" O4* O 0 1 N N N 57.405 40.397 9.653 -0.340 0.142 -1.130 "O4'" 1RB 17 1RB "C3'" C3* C 0 1 N N S 57.525 38.167 10.365 -0.285 1.986 0.356 "C3'" 1RB 18 1RB "O3'" O3* O 0 1 N N N 58.402 38.248 11.510 0.038 2.192 1.733 "O3'" 1RB 19 1RB "C2'" C2* C 0 1 N N R 56.152 38.717 10.655 0.996 1.997 -0.508 "C2'" 1RB 20 1RB "O2'" O2* O 0 1 N N N 55.702 38.225 11.919 2.149 2.213 0.308 "O2'" 1RB 21 1RB "C1'" C1* C 0 1 N N S 56.334 40.224 10.584 1.034 0.589 -1.141 "C1'" 1RB 22 1RB H2 H2 H 0 1 N N N 54.867 40.434 13.122 0.397 -1.402 0.815 H2 1RB 23 1RB H4 H4 H 0 1 N N N 58.383 43.224 15.411 5.231 -2.447 1.472 H4 1RB 24 1RB H5 H5 H 0 1 N N N 60.462 43.871 14.219 6.952 -1.261 0.210 H5 1RB 25 1RB H6 H6 H 0 1 N N N 60.856 43.125 11.792 6.335 0.478 -1.415 H6 1RB 26 1RB H7 H7 H 0 1 N N N 59.152 41.743 10.600 3.974 1.046 -1.791 H7 1RB 27 1RB HOP2 2HOP H 0 0 N N N 59.688 41.259 5.619 -6.130 -1.884 -0.436 HOP2 1RB 28 1RB HOP3 3HOP H 0 0 N N N 60.574 39.918 7.456 -4.789 -0.668 1.973 HOP3 1RB 29 1RB "H5'1" 1H5* H 0 0 N N N 57.752 37.645 7.583 -2.782 1.062 1.014 "H5'1" 1RB 30 1RB "H5'2" 2H5* H 0 0 N N N 56.362 38.569 7.795 -2.714 1.241 -0.755 "H5'2" 1RB 31 1RB "H4'" H4* H 0 1 N N N 59.059 39.083 9.117 -0.545 -0.096 0.938 "H4'" 1RB 32 1RB "H3'" H3* H 0 1 N N N 57.550 37.082 10.108 -0.985 2.747 0.011 "H3'" 1RB 33 1RB HO23 3HO2 H 0 0 N N N 58.136 37.667 12.213 0.427 3.075 1.799 HO23 1RB 34 1RB "H2'" H2* H 0 1 N N N 55.357 38.403 9.939 0.928 2.762 -1.282 "H2'" 1RB 35 1RB HO22 2HO2 H 0 0 N N N 54.837 38.572 12.102 2.039 3.080 0.723 HO22 1RB 36 1RB "H1'" H1* H 0 1 N N N 55.385 40.718 10.270 1.407 0.642 -2.164 "H1'" 1RB 37 # # 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 1RB N3 C2 DOUB Y N 1 1RB N3 C3A SING Y N 2 1RB N1 C2 SING Y N 3 1RB N1 C7A SING Y N 4 1RB N1 "C1'" SING N N 5 1RB C2 H2 SING N N 6 1RB C7A C3A DOUB Y N 7 1RB C7A C7 SING Y N 8 1RB C3A C4 SING Y N 9 1RB C4 C5 DOUB Y N 10 1RB C4 H4 SING N N 11 1RB C5 C6 SING Y N 12 1RB C5 H5 SING N N 13 1RB C6 C7 DOUB Y N 14 1RB C6 H6 SING N N 15 1RB C7 H7 SING N N 16 1RB P O1P DOUB N N 17 1RB P O2P SING N N 18 1RB P O3P SING N N 19 1RB P "O5'" SING N N 20 1RB O2P HOP2 SING N N 21 1RB O3P HOP3 SING N N 22 1RB "O5'" "C5'" SING N N 23 1RB "C5'" "C4'" SING N N 24 1RB "C5'" "H5'1" SING N N 25 1RB "C5'" "H5'2" SING N N 26 1RB "C4'" "O4'" SING N N 27 1RB "C4'" "C3'" SING N N 28 1RB "C4'" "H4'" SING N N 29 1RB "O4'" "C1'" SING N N 30 1RB "C3'" "O3'" SING N N 31 1RB "C3'" "C2'" SING N N 32 1RB "C3'" "H3'" SING N N 33 1RB "O3'" HO23 SING N N 34 1RB "C2'" "O2'" SING N N 35 1RB "C2'" "C1'" SING N N 36 1RB "C2'" "H2'" SING N N 37 1RB "O2'" HO22 SING N N 38 1RB "C1'" "H1'" SING N N 39 # # 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 1RB SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1ccccc12)C(O)C3O" 1RB SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3ccccc23" 1RB SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3ccccc23" 1RB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O" 1RB SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)ncn2C3C(C(C(O3)COP(=O)(O)O)O)O" 1RB InChI InChI 1.03 "InChI=1S/C12H15N2O7P/c15-10-9(5-20-22(17,18)19)21-12(11(10)16)14-6-13-7-3-1-2-4-8(7)14/h1-4,6,9-12,15-16H,5H2,(H2,17,18,19)/t9-,10-,11-,12+/m1/s1" 1RB InChIKey InChI 1.03 YPYFPLLZCVEYCS-KKOKHZNYSA-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 1RB "SYSTEMATIC NAME" ACDLabs 10.04 "1-(5-O-phosphono-alpha-D-ribofuranosyl)-1H-benzimidazole" 1RB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5S)-5-(benzimidazol-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen 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 1RB "Create component" 2002-03-19 RCSB 1RB "Modify descriptor" 2011-06-04 RCSB 1RB "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 1RB _pdbx_chem_comp_synonyms.name "ALPHA-RIBAZOLE-5'-PHOSPHATE DERIVATIVE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##