data_JKM # _chem_comp.id JKM _chem_comp.name ;1-[(2S,3aS,4S,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4( 1H,3H)-dione ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H11 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Uridine 2',3'-cyclophosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-02-24 _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 306.166 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JKM _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 4DVL _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 JKM P P P 0 1 N N N 9.890 20.249 12.688 -2.550 -1.596 -0.239 P JKM 1 JKM N1 N1 N 0 1 N N N 10.913 24.275 15.576 1.746 0.308 0.304 N1 JKM 2 JKM C2 C2 C 0 1 N N N 12.397 24.474 15.466 2.216 -0.917 0.601 C2 JKM 3 JKM O2 O2 O 0 1 N N N 13.007 24.188 14.469 1.488 -1.722 1.148 O2 JKM 4 JKM N3 N3 N 0 1 N N N 13.071 25.027 16.584 3.481 -1.265 0.299 N3 JKM 5 JKM C4 C4 C 0 1 N N N 12.364 25.326 17.700 4.301 -0.383 -0.308 C4 JKM 6 JKM O4 O4 O 0 1 N N N 12.950 25.845 18.785 5.446 -0.697 -0.582 O4 JKM 7 JKM C5 C5 C 0 1 N N N 10.952 25.132 17.867 3.819 0.910 -0.625 C5 JKM 8 JKM C6 C6 C 0 1 N N N 10.282 24.635 16.794 2.546 1.231 -0.312 C6 JKM 9 JKM "C1'" "C1'" C 0 1 N N S 9.900 23.748 14.572 0.362 0.655 0.639 "C1'" JKM 10 JKM "C2'" "C2'" C 0 1 N N S 10.172 22.494 13.730 -0.608 -0.240 -0.105 "C2'" JKM 11 JKM "O2'" "O2'" O 0 1 N N N 10.096 21.176 14.141 -1.012 -1.513 0.336 "O2'" JKM 12 JKM O20 O20 O 0 1 N N N 8.986 21.509 11.981 -2.831 -0.063 -0.777 O20 JKM 13 JKM O2P O2P O 0 1 N N N 8.796 19.121 13.020 -3.578 -1.984 0.938 O2P JKM 14 JKM "C3'" "C3'" C 0 1 N N R 8.834 22.559 12.887 -1.905 0.638 0.029 "C3'" JKM 15 JKM O3P O3P O 0 1 N N N 11.116 19.722 12.014 -2.641 -2.567 -1.352 O3P JKM 16 JKM "C4'" "C4'" C 0 1 N N R 8.693 24.053 12.555 -1.344 1.996 -0.319 "C4'" JKM 17 JKM "O4'" "O4'" O 0 1 N N N 9.437 24.709 13.589 0.032 1.984 0.145 "O4'" JKM 18 JKM "C5'" "C5'" C 0 1 N N N 7.173 24.350 12.668 -2.133 3.094 0.398 "C5'" JKM 19 JKM "O5'" "O5'" O 0 1 N N N 6.515 23.821 11.541 -1.666 4.374 -0.031 "O5'" JKM 20 JKM H5 H5 H 0 1 N N N 10.450 25.368 18.794 4.461 1.629 -1.112 H5 JKM 21 JKM H6 H6 H 0 1 N N N 9.212 24.507 16.873 2.161 2.212 -0.547 H6 JKM 22 JKM "H1'" "H1'" H 0 1 N N N 9.015 23.493 15.174 0.200 0.589 1.715 "H1'" JKM 23 JKM "H2'" "H2'" H 0 1 N N N 11.029 22.671 13.063 -0.328 -0.288 -1.157 "H2'" JKM 24 JKM HO2P HO2P H 0 0 N N N 9.113 18.275 12.726 -4.499 -2.046 0.650 HO2P JKM 25 JKM "H3'" "H3'" H 0 1 N N N 8.018 22.308 13.581 -2.243 0.644 1.065 "H3'" JKM 26 JKM "H4'" "H4'" H 0 1 N N N 9.068 24.277 11.546 -1.377 2.152 -1.397 "H4'" JKM 27 JKM "H5'" "H5'" H 0 1 N N N 6.773 23.883 13.581 -3.192 2.994 0.159 "H5'" JKM 28 JKM "H5'A" "H5'A" H 0 0 N N N 7.012 25.437 12.712 -1.993 2.998 1.475 "H5'A" JKM 29 JKM "HO5'" "HO5'" H 0 0 N N N 5.584 24.000 11.604 -2.123 5.119 0.383 "HO5'" JKM 30 JKM HN3 HN3 H 0 1 N N N 14.056 25.194 16.549 3.804 -2.152 0.520 HN3 JKM 31 # # 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 JKM O20 P SING N N 1 JKM O3P P DOUB N N 2 JKM P O2P SING N N 3 JKM P "O2'" SING N N 4 JKM "C1'" N1 SING N N 5 JKM C2 N1 SING N N 6 JKM N1 C6 SING N N 7 JKM O2 C2 DOUB N N 8 JKM C2 N3 SING N N 9 JKM N3 C4 SING N N 10 JKM C4 C5 SING N N 11 JKM C4 O4 DOUB N N 12 JKM C6 C5 DOUB N N 13 JKM C5 H5 SING N N 14 JKM C6 H6 SING N N 15 JKM "O4'" "C1'" SING N N 16 JKM "C2'" "C1'" SING N N 17 JKM "C1'" "H1'" SING N N 18 JKM "C3'" "C2'" SING N N 19 JKM "C2'" "O2'" SING N N 20 JKM "C2'" "H2'" SING N N 21 JKM O20 "C3'" SING N N 22 JKM O2P HO2P SING N N 23 JKM "C4'" "C3'" SING N N 24 JKM "C3'" "H3'" SING N N 25 JKM "C4'" "C5'" SING N N 26 JKM "C4'" "O4'" SING N N 27 JKM "C4'" "H4'" SING N N 28 JKM "O5'" "C5'" SING N N 29 JKM "C5'" "H5'" SING N N 30 JKM "C5'" "H5'A" SING N N 31 JKM "O5'" "HO5'" SING N N 32 JKM N3 HN3 SING N N 33 # # 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 JKM SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C2OC(C3OP(=O)(O)OC23)CO" JKM InChI InChI 1.03 "InChI=1S/C9H11N2O8P/c12-3-4-6-7(19-20(15,16)18-6)8(17-4)11-2-1-5(13)10-9(11)14/h1-2,4,6-8,12H,3H2,(H,15,16)(H,10,13,14)/t4-,6-,7+,8+/m1/s1" JKM InChIKey InChI 1.03 HWDMHJDYMFRXOX-GVYWOMJSSA-N JKM SMILES_CANONICAL CACTVS 3.370 "OC[C@H]1O[C@@H]([C@H]2O[P](O)(=O)O[C@H]12)N3C=CC(=O)NC3=O" JKM SMILES CACTVS 3.370 "OC[CH]1O[CH]([CH]2O[P](O)(=O)O[CH]12)N3C=CC(=O)NC3=O" JKM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)[C@@H]2[C@@H]3[C@@H]([C@H](O2)CO)O[P@@](=O)(O3)O" JKM SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C3C(C(O2)CO)OP(=O)(O3)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 JKM "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(2S,3aS,4S,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(1H,3H)-dione" JKM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "1-[(2S,3aS,4S,6R,6aR)-6-(hydroxymethyl)-2-oxidanyl-2-oxidanylidene-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site JKM "Create component" 2012-02-24 RCSB JKM "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id JKM _pdbx_chem_comp_synonyms.name "Uridine 2',3'-cyclophosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##