data_DBI # _chem_comp.id DBI _chem_comp.name "PHOSPHORIC ACID MONO-[5-(5,6-DIMETHYL-BENZOIMIDAZOL-1-YL)-4-HYDROXY-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H19 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms DIMETHYLBENZIMIDAZOLE-NUCLEOTIDE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-04-11 _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 358.284 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DBI _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 1ID8 _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 DBI P P P 0 1 N N N 0.209 -16.172 -7.452 -1.243 -0.198 -4.125 P DBI 1 DBI O1P O1P O 0 1 N N N -0.181 -17.703 -7.503 -0.306 0.693 -4.843 O1P DBI 2 DBI O2P O2P O 0 1 N N N 1.259 -15.956 -6.291 -1.762 -1.348 -5.125 O2P DBI 3 DBI "O3'" "O3'" O 0 1 N N N -1.070 -15.271 -7.182 -0.489 -0.874 -2.874 "O3'" DBI 4 DBI "O5'" "O5'" O 0 1 N N N -4.211 -17.523 -6.534 3.586 0.940 -2.731 "O5'" DBI 5 DBI "C5'" "C5'" C 0 1 N N N -4.200 -16.260 -7.150 2.176 0.926 -2.963 "C5'" DBI 6 DBI "C4'" "C4'" C 0 1 N N R -3.337 -15.257 -6.376 1.481 0.160 -1.834 "C4'" DBI 7 DBI "O4'" "O4'" O 0 1 N N N -3.894 -15.000 -5.103 1.714 0.810 -0.575 "O4'" DBI 8 DBI "C1'" "C1'" C 0 1 N N S -2.863 -14.520 -4.261 0.545 0.716 0.247 "C1'" DBI 9 DBI N1 N1 N 0 1 Y N N -2.860 -13.057 -4.246 0.852 -0.040 1.463 N1 DBI 10 DBI C8 C8 C 0 1 Y N N -3.169 -12.228 -3.173 0.237 0.099 2.691 C8 DBI 11 DBI C7 C7 C 0 1 Y N N -3.623 -12.468 -1.907 -0.778 0.910 3.176 C7 DBI 12 DBI C6 C6 C 0 1 Y N N -3.763 -11.434 -0.974 -1.174 0.796 4.492 C6 DBI 13 DBI C11 C11 C 0 1 N N N -4.223 -11.758 0.418 -2.277 1.676 5.022 C11 DBI 14 DBI C10 C10 C 0 1 N N N -3.607 -8.944 -0.398 -1.000 -0.223 6.772 C10 DBI 15 DBI C5 C5 C 0 1 Y N N -3.480 -10.114 -1.357 -0.557 -0.116 5.335 C5 DBI 16 DBI C4 C4 C 0 1 Y N N -3.067 -9.877 -2.670 0.444 -0.924 4.874 C4 DBI 17 DBI C9 C9 C 0 1 Y N N -2.896 -10.895 -3.567 0.858 -0.829 3.544 C9 DBI 18 DBI N3 N3 N 0 1 Y N N -2.475 -10.938 -4.886 1.799 -1.473 2.807 N3 DBI 19 DBI C2 C2 C 0 1 Y N N -2.465 -12.240 -5.238 1.795 -1.012 1.591 C2 DBI 20 DBI "C2'" "C2'" C 0 1 N N R -1.565 -15.188 -4.747 -0.541 -0.017 -0.566 "C2'" DBI 21 DBI "O2'" "O2'" O 0 1 N N N -0.437 -14.344 -4.701 -0.576 -1.407 -0.236 "O2'" DBI 22 DBI "C3'" "C3'" C 0 1 N N S -1.904 -15.721 -6.133 -0.055 0.191 -2.028 "C3'" DBI 23 DBI O3P O3P O 0 1 N N N 0.887 -15.764 -8.828 -2.499 0.657 -3.595 O3P DBI 24 DBI HO2 HO2 H 0 1 N N N 1.493 -15.035 -6.260 -2.207 -0.902 -5.858 HO2 DBI 25 DBI HO5 HO5 H 0 1 N N N -4.745 -18.144 -7.013 3.985 1.431 -3.463 HO5 DBI 26 DBI "H5'1" "1H5'" H 0 0 N N N -5.231 -15.912 -7.227 1.969 0.436 -3.914 "H5'1" DBI 27 DBI "H5'2" "2H5'" H 0 0 N N N -3.805 -16.397 -8.157 1.802 1.949 -2.992 "H5'2" DBI 28 DBI "H4'" "H4'" H 0 1 N N N -3.335 -14.314 -6.921 1.838 -0.868 -1.801 "H4'" DBI 29 DBI "H1'" "H1'" H 0 1 N N N -3.084 -14.880 -3.252 0.198 1.715 0.511 "H1'" DBI 30 DBI H7 H7 H 0 1 N N N -3.900 -13.476 -1.649 -1.259 1.626 2.526 H7 DBI 31 DBI H111 1H11 H 0 0 N N N -4.666 -12.752 0.475 -3.237 1.180 4.879 H111 DBI 32 DBI H112 2H11 H 0 0 N N N -4.948 -11.036 0.788 -2.117 1.860 6.084 H112 DBI 33 DBI H113 3H11 H 0 0 N N N -3.347 -11.734 1.061 -2.274 2.624 4.484 H113 DBI 34 DBI H101 1H10 H 0 0 N N N -2.746 -8.893 0.270 -0.412 0.459 7.385 H101 DBI 35 DBI H102 2H10 H 0 0 N N N -4.509 -8.990 0.210 -2.055 0.037 6.847 H102 DBI 36 DBI H103 3H10 H 0 0 N N N -3.604 -7.990 -0.931 -0.852 -1.245 7.122 H103 DBI 37 DBI H4 H4 H 0 1 N N N -2.869 -8.863 -2.965 0.915 -1.634 5.538 H4 DBI 38 DBI H2 H2 H 0 1 N N N -2.143 -12.576 -6.212 2.447 -1.350 0.799 H2 DBI 39 DBI "H2'" "H2'" H 0 1 N N N -1.337 -16.040 -4.101 -1.519 0.440 -0.413 "H2'" DBI 40 DBI HO21 1HO2 H 0 0 N N N -0.261 -14.087 -3.801 -0.884 -1.469 0.678 HO21 DBI 41 DBI "H3'" "H3'" H 0 1 N N N -1.884 -16.810 -6.101 -0.383 1.156 -2.415 "H3'" DBI 42 DBI HO3 HO3 H 0 1 N N N 1.121 -14.843 -8.797 -3.084 0.040 -3.134 HO3 DBI 43 # # 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 DBI P O1P DOUB N N 1 DBI P O2P SING N N 2 DBI P "O3'" SING N N 3 DBI P O3P SING N N 4 DBI O2P HO2 SING N N 5 DBI "O3'" "C3'" SING N N 6 DBI "O5'" "C5'" SING N N 7 DBI "O5'" HO5 SING N N 8 DBI "C5'" "C4'" SING N N 9 DBI "C5'" "H5'1" SING N N 10 DBI "C5'" "H5'2" SING N N 11 DBI "C4'" "O4'" SING N N 12 DBI "C4'" "C3'" SING N N 13 DBI "C4'" "H4'" SING N N 14 DBI "O4'" "C1'" SING N N 15 DBI "C1'" N1 SING N N 16 DBI "C1'" "C2'" SING N N 17 DBI "C1'" "H1'" SING N N 18 DBI N1 C8 SING Y N 19 DBI N1 C2 SING Y N 20 DBI C8 C7 DOUB Y N 21 DBI C8 C9 SING Y N 22 DBI C7 C6 SING Y N 23 DBI C7 H7 SING N N 24 DBI C6 C11 SING N N 25 DBI C6 C5 DOUB Y N 26 DBI C11 H111 SING N N 27 DBI C11 H112 SING N N 28 DBI C11 H113 SING N N 29 DBI C10 C5 SING N N 30 DBI C10 H101 SING N N 31 DBI C10 H102 SING N N 32 DBI C10 H103 SING N N 33 DBI C5 C4 SING Y N 34 DBI C4 C9 DOUB Y N 35 DBI C4 H4 SING N N 36 DBI C9 N3 SING Y N 37 DBI N3 C2 DOUB Y N 38 DBI C2 H2 SING N N 39 DBI "C2'" "O2'" SING N N 40 DBI "C2'" "C3'" SING N N 41 DBI "C2'" "H2'" SING N N 42 DBI "O2'" HO21 SING N N 43 DBI "C3'" "H3'" SING N N 44 DBI O3P HO3 SING N N 45 # # 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 DBI SMILES ACDLabs 10.04 "O=P(O)(O)OC3C(OC(n2cnc1cc(c(cc12)C)C)C3O)CO" DBI SMILES_CANONICAL CACTVS 3.341 "Cc1cc2ncn([C@H]3O[C@H](CO)[C@@H](O[P](O)(O)=O)[C@H]3O)c2cc1C" DBI SMILES CACTVS 3.341 "Cc1cc2ncn([CH]3O[CH](CO)[CH](O[P](O)(O)=O)[CH]3O)c2cc1C" DBI SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O3)CO)OP(=O)(O)O)O" DBI SMILES "OpenEye OEToolkits" 1.5.0 "Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)O)O" DBI InChI InChI 1.03 "InChI=1S/C14H19N2O7P/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-12(18)13(11(5-17)22-14)23-24(19,20)21/h3-4,6,11-14,17-18H,5H2,1-2H3,(H2,19,20,21)/t11-,12-,13-,14+/m1/s1" DBI InChIKey InChI 1.03 JIABVZWSYKDHDJ-SYQHCUMBSA-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 DBI "SYSTEMATIC NAME" ACDLabs 10.04 "5,6-dimethyl-1-(3-O-phosphono-alpha-D-ribofuranosyl)-1H-benzimidazole" DBI "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5S)-5-(5,6-dimethylbenzimidazol-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] 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 DBI "Create component" 2001-04-11 RCSB DBI "Modify descriptor" 2011-06-04 RCSB DBI "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DBI _pdbx_chem_comp_synonyms.name DIMETHYLBENZIMIDAZOLE-NUCLEOTIDE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##