data_DRM # _chem_comp.id DRM _chem_comp.name "{[(1R,2S)-2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOPENTYL]OXY}METHYLPHOSPHONIC ACID" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O6 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms "1-TRANS-(2-PHOSPHONOMETHOXYCYCLOPENTYL)URACIL; PMCP-U" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-09-17 _chem_comp.pdbx_modified_date 2020-05-27 _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 290.210 _chem_comp.one_letter_code U _chem_comp.three_letter_code DRM _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 1Q92 _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 DRM OP2 O2P O 0 1 N N N 17.362 37.703 27.365 -2.216 -0.726 3.419 OP2 DRM 1 DRM P P P 0 1 N N N 17.457 39.170 27.140 -1.369 -0.074 2.216 P DRM 2 DRM OP1 O1P O 0 1 N N N 17.930 39.988 28.360 -2.106 1.084 1.665 OP1 DRM 3 DRM OP3 O3P O 0 1 N Y N 18.303 39.546 25.897 -1.149 -1.170 1.058 OP3 DRM 4 DRM "C6'" C6* C 0 1 N N N 15.728 39.652 26.800 0.250 0.479 2.844 "C6'" DRM 5 DRM "O5'" O5* O 0 1 N N N 15.624 41.065 26.828 0.940 1.193 1.816 "O5'" DRM 6 DRM "C5'" C5* C 0 1 N N R 14.315 41.584 26.537 1.456 0.216 0.910 "C5'" DRM 7 DRM "C4'" C4* C 0 1 N N N 14.675 43.022 26.347 2.853 -0.267 1.370 "C4'" DRM 8 DRM "C3'" C3* C 0 1 N N N 14.117 43.796 27.501 3.485 -0.789 0.056 "C3'" DRM 9 DRM "C2'" C2* C 0 1 N N N 13.045 42.969 28.117 3.001 0.206 -1.017 "C2'" DRM 10 DRM "C1'" C1* C 0 1 N N R 13.316 41.521 27.726 1.707 0.845 -0.475 "C1'" DRM 11 DRM N1 N1 N 0 1 N N N 12.125 40.691 27.466 0.589 0.554 -1.376 N1 DRM 12 DRM C6 C6 C 0 1 N N N 11.312 40.994 26.417 -0.110 1.584 -1.942 C6 DRM 13 DRM C5 C5 C 0 1 N N N 10.236 40.179 26.139 -1.141 1.316 -2.772 C5 DRM 14 DRM C4 C4 C 0 1 N N N 9.967 39.045 26.927 -1.477 -0.033 -3.039 C4 DRM 15 DRM O4 O4 O 0 1 N N N 9.004 38.314 26.676 -2.402 -0.300 -3.785 O4 DRM 16 DRM N3 N3 N 0 1 N N N 10.770 38.744 27.988 -0.763 -1.019 -2.461 N3 DRM 17 DRM C2 C2 C 0 1 N N N 11.833 39.561 28.252 0.262 -0.723 -1.642 C2 DRM 18 DRM O2 O2 O 0 1 N N N 12.583 39.358 29.234 0.898 -1.624 -1.127 O2 DRM 19 DRM HOP2 2HOP H 0 0 N N N 17.070 37.199 26.613 -3.063 -1.005 3.045 HOP2 DRM 20 DRM HOP3 3HOP H 0 0 N N N 18.363 40.483 25.753 -0.666 -1.906 1.458 HOP3 DRM 21 DRM "H6'1" 1H6* H 0 0 N N N 15.347 39.218 25.845 0.839 -0.387 3.143 "H6'1" DRM 22 DRM "H6'2" 2H6* H 0 0 N N N 15.007 39.160 27.494 0.102 1.132 3.704 "H6'2" DRM 23 DRM "H5'" H5* H 0 1 N N N 13.813 41.031 25.708 0.769 -0.626 0.827 "H5'" DRM 24 DRM "H4'1" 1H4* H 0 0 N N N 15.770 43.177 26.213 2.763 -1.070 2.101 "H4'1" DRM 25 DRM "H4'2" 2H4* H 0 0 N N N 14.345 43.422 25.359 3.434 0.561 1.775 "H4'2" DRM 26 DRM "H3'1" 1H3* H 0 0 N N N 14.898 44.110 28.232 3.126 -1.794 -0.166 "H3'1" DRM 27 DRM "H3'2" 2H3* H 0 0 N N N 13.768 44.815 27.213 4.573 -0.777 0.124 "H3'2" DRM 28 DRM "H2'" 1H2* H 0 1 N N N 12.958 43.115 29.218 2.793 -0.319 -1.949 "H2'" DRM 29 DRM "H2''" 2H2* H 0 0 N N N 12.018 43.310 27.846 3.757 0.974 -1.183 "H2''" DRM 30 DRM "H1'" H1* H 0 1 N N N 13.751 40.977 28.596 1.836 1.923 -0.377 "H1'" DRM 31 DRM H6 H6 H 0 1 N N N 11.521 41.885 25.802 0.159 2.607 -1.726 H6 DRM 32 DRM H5 H5 H 0 1 N N N 9.588 40.435 25.283 -1.702 2.119 -3.226 H5 DRM 33 DRM H3 H3 H 0 1 N N N 10.580 37.927 28.569 -0.987 -1.946 -2.639 H3 DRM 34 # 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 DRM OP2 P SING N N 1 DRM OP2 HOP2 SING N N 2 DRM P OP1 DOUB N N 3 DRM P OP3 SING N N 4 DRM P "C6'" SING N N 5 DRM OP3 HOP3 SING N N 6 DRM "C6'" "O5'" SING N N 7 DRM "C6'" "H6'1" SING N N 8 DRM "C6'" "H6'2" SING N N 9 DRM "O5'" "C5'" SING N N 10 DRM "C5'" "C4'" SING N N 11 DRM "C5'" "C1'" SING N N 12 DRM "C5'" "H5'" SING N N 13 DRM "C4'" "C3'" SING N N 14 DRM "C4'" "H4'1" SING N N 15 DRM "C4'" "H4'2" SING N N 16 DRM "C3'" "C2'" SING N N 17 DRM "C3'" "H3'1" SING N N 18 DRM "C3'" "H3'2" SING N N 19 DRM "C2'" "C1'" SING N N 20 DRM "C2'" "H2'" SING N N 21 DRM "C2'" "H2''" SING N N 22 DRM "C1'" N1 SING N N 23 DRM "C1'" "H1'" SING N N 24 DRM N1 C6 SING N N 25 DRM N1 C2 SING N N 26 DRM C6 C5 DOUB N N 27 DRM C6 H6 SING N N 28 DRM C5 C4 SING N N 29 DRM C5 H5 SING N N 30 DRM C4 O4 DOUB N N 31 DRM C4 N3 SING N N 32 DRM N3 C2 SING N N 33 DRM N3 H3 SING N N 34 DRM C2 O2 DOUB N N 35 # 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 DRM SMILES ACDLabs 10.04 "O=P(O)(O)COC2CCCC2N1C=CC(=O)NC1=O" DRM SMILES_CANONICAL CACTVS 3.341 "O[P](O)(=O)CO[C@@H]1CCC[C@H]1N2C=CC(=O)NC2=O" DRM SMILES CACTVS 3.341 "O[P](O)(=O)CO[CH]1CCC[CH]1N2C=CC(=O)NC2=O" DRM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@H]([C@@H](C1)OCP(=O)(O)O)N2C=CC(=O)NC2=O" DRM SMILES "OpenEye OEToolkits" 1.5.0 "C1CC(C(C1)OCP(=O)(O)O)N2C=CC(=O)NC2=O" DRM InChI InChI 1.03 "InChI=1S/C10H15N2O6P/c13-9-4-5-12(10(14)11-9)7-2-1-3-8(7)18-6-19(15,16)17/h4-5,7-8H,1-3,6H2,(H,11,13,14)(H2,15,16,17)/t7-,8-/m1/s1" DRM InChIKey InChI 1.03 KKXMDNJBVSYDQL-HTQZYQBOSA-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 DRM "SYSTEMATIC NAME" ACDLabs 10.04 "({[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}methyl)phosphonic acid" DRM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R,2R)-2-(2,4-dioxopyrimidin-1-yl)cyclopentyl]oxymethylphosphonic 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 DRM "Create component" 2003-09-17 RCSB DRM "Modify descriptor" 2011-06-04 RCSB DRM "Modify synonyms" 2020-05-27 PDBE # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 DRM "1-TRANS-(2-PHOSPHONOMETHOXYCYCLOPENTYL)URACIL" ? ? 2 DRM PMCP-U ? ? #