data_2GF # _chem_comp.id 2GF _chem_comp.name "[(2R,5R)-5-(4-amino-5-chloro-2-oxopyrimidin-1(2H)-yl)-3-oxotetrahydrofuran-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H11 Cl N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-CHLORO DEOXYCYTIDINE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-10-15 _chem_comp.pdbx_modified_date 2021-03-01 _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 339.626 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2GF _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4MGW _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 2GF P P P 0 1 N N N -0.317 5.106 13.671 4.443 -1.129 -0.193 P 2GF 1 2GF OP1 O1P O 0 1 N N N -1.784 5.106 13.484 5.760 -0.209 -0.084 O1P 2GF 2 2GF OP2 O2P O 0 1 N N N -0.054 6.148 14.696 4.163 -1.748 1.121 O2P 2GF 3 2GF "O5'" "O5'" O 0 1 N N N 0.362 3.752 13.846 3.190 -0.221 -0.637 "O5'" 2GF 4 2GF "C5'" "C5'" C 0 1 N N N 0.048 2.785 12.952 2.658 0.824 0.180 "C5'" 2GF 5 2GF "C4'" "C4'" C 0 1 N N R 1.184 1.804 12.741 1.478 1.482 -0.538 "C4'" 2GF 6 2GF "O4'" "O4'" O 0 1 N N N 2.385 2.425 12.586 0.391 0.548 -0.644 "O4'" 2GF 7 2GF "C3'" "C3'" C 0 1 N N N 1.309 0.867 13.858 0.986 2.671 0.265 "C3'" 2GF 8 2GF "O3'" "O3'" O 0 1 N N N 0.392 0.116 14.135 1.614 3.649 0.593 "O3'" 2GF 9 2GF "C2'" "C2'" C 0 1 N N N 2.670 0.998 14.413 -0.475 2.360 0.567 "C2'" 2GF 10 2GF "C1'" "C1'" C 0 1 N N R 3.343 1.638 13.224 -0.825 1.319 -0.526 "C1'" 2GF 11 2GF N1 N1 N 0 1 N N N 4.364 2.562 13.563 -1.938 0.469 -0.094 N1 2GF 12 2GF C2 C2 C 0 1 N N N 5.675 2.408 13.112 -1.817 -0.276 1.020 C2 2GF 13 2GF O2 O2 O 0 1 N N N 5.968 1.314 12.339 -0.779 -0.236 1.659 O2 2GF 14 2GF N3 N3 N 0 1 N N N 6.710 3.339 13.438 -2.812 -1.057 1.436 N3 2GF 15 2GF C4 C4 C 0 1 N N N 6.385 4.406 14.213 -3.952 -1.120 0.760 C4 2GF 16 2GF N4 N4 N 0 1 N N N 7.374 5.381 14.552 -4.973 -1.931 1.200 N4 2GF 17 2GF C5 C5 C 0 1 N N N 5.043 4.568 14.676 -4.111 -0.352 -0.412 C5 2GF 18 2GF C6 C6 C 0 1 N N N 4.048 3.663 14.360 -3.092 0.442 -0.820 C6 2GF 19 2GF CL CL CL 0 0 N N N 4.661 5.931 15.686 -5.593 -0.417 -1.315 CL 2GF 20 2GF H1 H1 H 0 1 N N N -2.176 5.757 14.054 6.003 0.229 -0.911 H1 2GF 21 2GF "H5'1" "H5'1" H 0 0 N N N -0.193 3.259 11.989 2.320 0.408 1.129 "H5'1" 2GF 22 2GF "H5'2" "H5'2" H 0 0 N N N -0.830 2.235 13.320 3.432 1.569 0.365 "H5'2" 2GF 23 2GF "H4'" "H4'" H 0 1 N N N 0.953 1.224 11.835 1.785 1.809 -1.531 "H4'" 2GF 24 2GF "H2'2" "H2'2" H 0 0 N N N 3.111 0.021 14.661 -0.582 1.929 1.562 "H2'2" 2GF 25 2GF "H2'" "H2'" H 0 1 N N N 2.694 1.647 15.301 -1.090 3.254 0.466 "H2'" 2GF 26 2GF "H1'" "H1'" H 0 1 N N N 3.728 0.856 12.553 -1.062 1.812 -1.469 "H1'" 2GF 27 2GF H42 H42 H 0 1 N N N 8.311 5.280 14.218 -4.861 -2.458 2.007 H42 2GF 28 2GF H41 H41 H 0 1 N N N 7.129 6.164 15.123 -5.806 -1.975 0.704 H41 2GF 29 2GF H6 H6 H 0 1 N N N 3.041 3.805 14.724 -3.191 1.043 -1.711 H6 2GF 30 2GF OP3 O3P O 0 1 N Y N ? ? ? 4.684 -2.283 -1.290 O3P 2GF 31 2GF H4 H4 H 0 1 N N N ? ? ? 5.426 -2.869 -1.087 H4 2GF 32 # # 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 2GF O2 C2 DOUB N N 1 2GF "O4'" "C4'" SING N N 2 2GF "O4'" "C1'" SING N N 3 2GF "C4'" "C5'" SING N N 4 2GF "C4'" "C3'" SING N N 5 2GF "C5'" "O5'" SING N N 6 2GF C2 N3 SING N N 7 2GF C2 N1 SING N N 8 2GF "C1'" N1 SING N N 9 2GF "C1'" "C2'" SING N N 10 2GF N3 C4 DOUB N N 11 2GF OP1 P SING N N 12 2GF N1 C6 SING N N 13 2GF P "O5'" SING N N 14 2GF P OP2 DOUB N N 15 2GF "C3'" "O3'" DOUB N N 16 2GF "C3'" "C2'" SING N N 17 2GF C4 N4 SING N N 18 2GF C4 C5 SING N N 19 2GF C6 C5 DOUB N N 20 2GF C5 CL SING N N 21 2GF OP1 H1 SING N N 22 2GF "C5'" "H5'1" SING N N 23 2GF "C5'" "H5'2" SING N N 24 2GF "C4'" "H4'" SING N N 25 2GF "C2'" "H2'2" SING N N 26 2GF "C2'" "H2'" SING N N 27 2GF "C1'" "H1'" SING N N 28 2GF N4 H42 SING N N 29 2GF N4 H41 SING N N 30 2GF C6 H6 SING N N 31 2GF P OP3 SING N N 32 2GF OP3 H4 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 2GF SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(Cl)=C1)CC2=O" 2GF InChI InChI 1.03 "InChI=1S/C9H11ClN3O7P/c10-4-2-13(9(15)12-8(4)11)7-1-5(14)6(20-7)3-19-21(16,17)18/h2,6-7H,1,3H2,(H2,11,12,15)(H2,16,17,18)/t6-,7-/m1/s1" 2GF InChIKey InChI 1.03 ALLUETJMPVZHQY-RNFRBKRXSA-N 2GF SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1Cl)[C@H]2CC(=O)[C@@H](CO[P](O)(O)=O)O2" 2GF SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1Cl)[CH]2CC(=O)[CH](CO[P](O)(O)=O)O2" 2GF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H](O[C@@H](C1=O)COP(=O)(O)O)N2C=C(C(=NC2=O)N)Cl" 2GF SMILES "OpenEye OEToolkits" 1.7.6 "C1C(OC(C1=O)COP(=O)(O)O)N2C=C(C(=NC2=O)N)Cl" # # 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 2GF "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,5R)-5-(4-amino-5-chloro-2-oxopyrimidin-1(2H)-yl)-3-oxotetrahydrofuran-2-yl]methyl dihydrogen phosphate" 2GF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,5R)-5-(4-azanyl-5-chloranyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanylidene-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 2GF "Create component" 2013-10-15 RCSB 2GF "Initial release" 2013-11-06 RCSB 2GF "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2GF _pdbx_chem_comp_synonyms.name "5-CHLORO DEOXYCYTIDINE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##