data_NBM # _chem_comp.id NBM _chem_comp.name "6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H17 N5 O6 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-03-21 _chem_comp.pdbx_modified_date 2019-06-28 _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 419.412 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NBM _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 6OB6 _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 NBM C01 C1 C 0 1 Y N N 11.111 30.019 31.673 -5.142 -0.690 -1.049 C01 NBM 1 NBM C02 C2 C 0 1 Y N N 12.219 29.215 31.773 -6.432 -0.225 -1.224 C02 NBM 2 NBM C03 C3 C 0 1 Y N N 12.947 29.155 32.974 -7.114 0.340 -0.162 C03 NBM 3 NBM C04 C4 C 0 1 Y N N 12.525 29.923 34.085 -6.505 0.440 1.075 C04 NBM 4 NBM C05 C5 C 0 1 Y N N 11.393 30.742 33.982 -5.215 -0.026 1.250 C05 NBM 5 NBM C06 C6 C 0 1 Y N N 10.685 30.807 32.799 -4.534 -0.590 0.188 C06 NBM 6 NBM C07 C7 C 0 1 N N N 9.413 31.724 32.688 -3.128 -1.097 0.380 C07 NBM 7 NBM C09 C8 C 0 1 Y N N 9.850 34.601 32.264 -0.436 -0.610 0.324 C09 NBM 8 NBM C11 C9 C 0 1 Y N N 10.116 35.780 34.278 0.704 -2.527 0.920 C11 NBM 9 NBM C13 C10 C 0 1 Y N N 10.205 36.994 32.256 1.973 -0.673 0.431 C13 NBM 10 NBM C14 C11 C 0 1 Y N N 9.999 35.827 31.520 0.796 0.052 0.178 C14 NBM 11 NBM C16 C12 C 0 1 Y N N 10.193 37.538 30.105 2.466 1.396 -0.149 C16 NBM 12 NBM C18 C13 C 0 1 N N R 10.545 39.398 31.791 4.436 -0.097 0.356 C18 NBM 13 NBM C19 C14 C 0 1 N N R 11.752 39.832 31.418 5.003 -0.679 -0.964 C19 NBM 14 NBM C20 C15 C 0 1 N N S 11.572 41.281 31.106 6.508 -0.329 -0.853 C20 NBM 15 NBM C21 C16 C 0 1 N N R 10.012 41.531 31.141 6.553 0.824 0.169 C21 NBM 16 NBM C23 C17 C 0 1 N N N 9.522 42.391 29.934 7.197 2.057 -0.468 C23 NBM 17 NBM N10 N1 N 0 1 Y N N 9.915 34.613 33.601 -0.428 -1.887 0.693 N10 NBM 18 NBM N12 N2 N 0 1 Y N N 10.255 36.926 33.627 1.880 -1.948 0.796 N12 NBM 19 NBM N15 N3 N 0 1 Y N N 10.000 36.197 30.178 1.168 1.307 -0.171 N15 NBM 20 NBM N17 N4 N 0 1 Y N N 10.325 38.031 31.388 3.009 0.201 0.217 N17 NBM 21 NBM N27 N5 N 1 1 N N N 14.129 28.279 33.064 -8.495 0.839 -0.350 N27 NBM 22 NBM O22 O1 O 0 1 N N N 9.487 40.370 31.069 5.196 1.116 0.543 O22 NBM 23 NBM O24 O2 O 0 1 N N N 8.121 42.451 29.999 7.341 3.082 0.518 O24 NBM 24 NBM O25 O3 O 0 1 N N N 12.200 42.057 32.052 7.248 -1.453 -0.371 O25 NBM 25 NBM O26 O4 O 0 1 N N N 12.715 39.668 32.533 4.812 -2.093 -1.022 O26 NBM 26 NBM O28 O5 O 0 1 N N N 14.783 28.209 34.116 -9.031 0.751 -1.441 O28 NBM 27 NBM O29 O6 O -1 1 N N N 14.480 27.609 32.080 -9.095 1.337 0.585 O29 NBM 28 NBM S08 S1 S 0 1 N N N 9.590 32.999 31.416 -1.954 0.236 0.032 S08 NBM 29 NBM H011 H1 H 0 0 N N N 10.557 30.060 30.747 -4.612 -1.136 -1.877 H011 NBM 30 NBM H021 H2 H 0 0 N N N 12.533 28.625 30.924 -6.908 -0.302 -2.191 H021 NBM 31 NBM H041 H3 H 0 0 N N N 13.076 29.878 35.013 -7.037 0.881 1.904 H041 NBM 32 NBM H051 H4 H 0 0 N N N 11.073 31.325 34.833 -4.740 0.052 2.217 H051 NBM 33 NBM H071 H5 H 0 0 N N N 9.245 32.214 33.658 -3.000 -1.435 1.408 H071 NBM 34 NBM H072 H6 H 0 0 N N N 8.545 31.095 32.440 -2.945 -1.929 -0.301 H072 NBM 35 NBM H111 H7 H 0 0 N N N 10.162 35.770 35.357 0.665 -3.564 1.218 H111 NBM 36 NBM H161 H8 H 0 0 N N N 10.236 38.121 29.197 3.030 2.286 -0.386 H161 NBM 37 NBM H181 H9 H 0 0 N N N 10.401 39.494 32.877 4.605 -0.787 1.183 H181 NBM 38 NBM H191 H10 H 0 0 N N N 12.122 39.305 30.526 4.554 -0.191 -1.829 H191 NBM 39 NBM H201 H11 H 0 0 N N N 11.942 41.495 30.093 6.895 -0.001 -1.817 H201 NBM 40 NBM H211 H12 H 0 0 N N N 9.765 42.059 32.074 7.123 0.519 1.046 H211 NBM 41 NBM H231 H13 H 0 0 N N N 9.834 41.923 28.989 8.178 1.792 -0.862 H231 NBM 42 NBM H232 H14 H 0 0 N N N 9.945 43.404 29.999 6.566 2.420 -1.279 H232 NBM 43 NBM H241 H15 H 0 0 N N N 7.792 42.970 29.274 7.744 3.895 0.185 H241 NBM 44 NBM H251 H16 H 0 0 N N N 13.136 41.898 32.022 8.187 -1.273 -0.227 H251 NBM 45 NBM H261 H17 H 0 0 N N N 12.824 38.744 32.725 5.150 -2.503 -1.830 H261 NBM 46 # # 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 NBM C23 O24 SING N N 1 NBM C23 C21 SING N N 2 NBM C16 N15 DOUB Y N 3 NBM C16 N17 SING Y N 4 NBM N15 C14 SING Y N 5 NBM O22 C21 SING N N 6 NBM O22 C18 SING N N 7 NBM C20 C21 SING N N 8 NBM C20 C19 SING N N 9 NBM C20 O25 SING N N 10 NBM N17 C18 SING N N 11 NBM N17 C13 SING Y N 12 NBM S08 C09 SING N N 13 NBM S08 C07 SING N N 14 NBM C19 C18 SING N N 15 NBM C19 O26 SING N N 16 NBM C14 C13 DOUB Y N 17 NBM C14 C09 SING Y N 18 NBM C01 C02 DOUB Y N 19 NBM C01 C06 SING Y N 20 NBM C02 C03 SING Y N 21 NBM O29 N27 SING N N 22 NBM C13 N12 SING Y N 23 NBM C09 N10 DOUB Y N 24 NBM C07 C06 SING N N 25 NBM C06 C05 DOUB Y N 26 NBM C03 N27 SING N N 27 NBM C03 C04 DOUB Y N 28 NBM N27 O28 DOUB N N 29 NBM N10 C11 SING Y N 30 NBM N12 C11 DOUB Y N 31 NBM C05 C04 SING Y N 32 NBM C01 H011 SING N N 33 NBM C02 H021 SING N N 34 NBM C04 H041 SING N N 35 NBM C05 H051 SING N N 36 NBM C07 H071 SING N N 37 NBM C07 H072 SING N N 38 NBM C11 H111 SING N N 39 NBM C16 H161 SING N N 40 NBM C18 H181 SING N N 41 NBM C19 H191 SING N N 42 NBM C20 H201 SING N N 43 NBM C21 H211 SING N N 44 NBM C23 H231 SING N N 45 NBM C23 H232 SING N N 46 NBM O24 H241 SING N N 47 NBM O25 H251 SING N N 48 NBM O26 H261 SING N N 49 # # 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 NBM SMILES ACDLabs 12.01 "c1cc([N+](=O)[O-])ccc1CSc2ncnc3c2ncn3C4C(O)C(C(CO)O4)O" NBM InChI InChI 1.03 "InChI=1S/C17H17N5O6S/c23-5-11-13(24)14(25)17(28-11)21-8-20-12-15(21)18-7-19-16(12)29-6-9-1-3-10(4-2-9)22(26)27/h1-4,7-8,11,13-14,17,23-25H,5-6H2/t11-,13-,14-,17-/m1/s1" NBM InChIKey InChI 1.03 DYCJFJRCWPVDHY-LSCFUAHRSA-N NBM SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(SCc4ccc(cc4)[N+]([O-])=O)ncnc23" NBM SMILES CACTVS 3.385 "OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(SCc4ccc(cc4)[N+]([O-])=O)ncnc23" NBM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CSc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)CO)O)O)[N+](=O)[O-]" NBM SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CSc2c3c(ncn2)n(cn3)C4C(C(C(O4)CO)O)O)[N+](=O)[O-]" # # 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 NBM "SYSTEMATIC NAME" ACDLabs 12.01 "6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine" NBM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-5-[6-[(4-nitrophenyl)methylsulfanyl]purin-9-yl]oxolane-3,4-diol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site NBM "Create component" 2019-03-21 RCSB NBM "Initial release" 2019-07-03 RCSB ##