data_DV3 # _chem_comp.id DV3 _chem_comp.name 1,4-anhydro-2-deoxy-5-O-thiophosphono-D-erythro-pentitol _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C5 H11 O5 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-11-22 _chem_comp.pdbx_modified_date 2018-08-10 _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 214.177 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DV3 _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 6BOS _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 DV3 "O5'" O1 O 0 1 N N N -2.914 -39.567 2.045 -0.644 -0.323 -0.572 "O5'" DV3 1 DV3 P P1 P 0 1 N N N -2.104 -39.152 3.463 -2.203 -0.375 -0.174 P DV3 2 DV3 SP3 S1 S 0 1 N N N -1.883 -37.079 3.601 -2.706 1.360 0.936 SP3 DV3 3 DV3 OP2 O2 O 0 1 N N N -0.752 -39.799 3.453 -2.463 -1.578 0.647 OP2 DV3 4 DV3 OP3 O3 O 0 1 N N N -2.911 -39.645 4.624 -3.097 -0.434 -1.511 OP3 DV3 5 DV3 "C2'" C1 C 0 1 N N N -3.596 -40.103 -1.854 3.735 0.832 0.549 "C2'" DV3 6 DV3 "C5'" C2 C 0 1 N N N -3.033 -38.606 1.008 0.408 -0.369 0.394 "C5'" DV3 7 DV3 "C4'" C3 C 0 1 N N R -4.265 -38.934 0.119 1.760 -0.301 -0.320 "C4'" DV3 8 DV3 "O4'" O4 O 0 1 N N N -4.278 -38.098 -0.869 1.921 0.987 -0.939 "O4'" DV3 9 DV3 "C1'" C4 C 0 1 N N N -4.188 -38.958 -2.227 3.324 1.318 -0.864 "C1'" DV3 10 DV3 "C3'" C5 C 0 1 N N S -4.108 -40.389 -0.477 2.901 -0.464 0.702 "C3'" DV3 11 DV3 "O3'" O5 O 0 1 N N N -5.357 -40.969 -0.595 3.695 -1.609 0.386 "O3'" DV3 12 DV3 H1 H1 H 0 1 N N N -0.590 -36.947 3.640 -2.424 2.359 0.080 H1 DV3 13 DV3 H2 H2 H 0 1 N N N -2.400 -40.272 5.122 -4.049 -0.467 -1.347 H2 DV3 14 DV3 H3 H3 H 0 1 N N N -3.867 -40.918 -2.542 4.802 0.615 0.591 H3 DV3 15 DV3 H4 H4 H 0 1 N N N -2.503 -39.984 -1.840 3.459 1.564 1.309 H4 DV3 16 DV3 H5 H5 H 0 1 N N N -2.123 -38.622 0.390 0.314 0.477 1.074 H5 DV3 17 DV3 H6 H6 H 0 1 N N N -3.158 -37.607 1.450 0.343 -1.299 0.958 H6 DV3 18 DV3 H7 H7 H 0 1 N N N -5.176 -38.896 0.734 1.820 -1.084 -1.075 H7 DV3 19 DV3 H8 H8 H 0 1 N N N -3.583 -38.434 -2.981 3.470 2.395 -0.957 H8 DV3 20 DV3 H9 H9 H 0 1 N N N -5.192 -39.152 -2.633 3.886 0.786 -1.632 H9 DV3 21 DV3 H10 H10 H 0 1 N N N -3.394 -40.980 0.115 2.500 -0.543 1.712 H10 DV3 22 DV3 H11 H11 H 0 1 N N N -5.701 -41.159 0.270 4.462 -1.727 0.963 H11 DV3 23 # 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 DV3 "C1'" "C2'" SING N N 1 DV3 "C1'" "O4'" SING N N 2 DV3 "C2'" "C3'" SING N N 3 DV3 "O4'" "C4'" SING N N 4 DV3 "O3'" "C3'" SING N N 5 DV3 "C3'" "C4'" SING N N 6 DV3 "C4'" "C5'" SING N N 7 DV3 "C5'" "O5'" SING N N 8 DV3 "O5'" P SING N N 9 DV3 OP2 P DOUB N N 10 DV3 P SP3 SING N N 11 DV3 P OP3 SING N N 12 DV3 SP3 H1 SING N N 13 DV3 OP3 H2 SING N N 14 DV3 "C2'" H3 SING N N 15 DV3 "C2'" H4 SING N N 16 DV3 "C5'" H5 SING N N 17 DV3 "C5'" H6 SING N N 18 DV3 "C4'" H7 SING N N 19 DV3 "C1'" H8 SING N N 20 DV3 "C1'" H9 SING N N 21 DV3 "C3'" H10 SING N N 22 DV3 "O3'" H11 SING N N 23 # 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 DV3 SMILES ACDLabs 12.01 "O(P(S)(O)=O)CC1OCCC1O" DV3 InChI InChI 1.03 "InChI=1S/C5H11O5PS/c6-4-1-2-9-5(4)3-10-11(7,8)12/h4-6H,1-3H2,(H2,7,8,12)/t4-,5+/m0/s1" DV3 InChIKey InChI 1.03 PPLIRDZWRNAVLB-CRCLSJGQSA-N DV3 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1CCO[C@@H]1CO[P](O)(S)=O" DV3 SMILES CACTVS 3.385 "O[CH]1CCO[CH]1CO[P](O)(S)=O" DV3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1CO[C@@H]([C@H]1O)COP(=O)(O)S" DV3 SMILES "OpenEye OEToolkits" 2.0.6 "C1COC(C1O)COP(=O)(O)S" # 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 DV3 "SYSTEMATIC NAME" ACDLabs 12.01 1,4-anhydro-2-deoxy-5-O-thiophosphono-D-erythro-pentitol DV3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S})-3-oxidanyloxolan-2-yl]methoxy-sulfanyl-phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DV3 "Create component" 2017-11-22 RCSB DV3 "Initial release" 2018-08-15 RCSB #