data_UMP # _chem_comp.id UMP _chem_comp.name ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms DUMP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2024-09-27 _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 308.182 _chem_comp.one_letter_code U _chem_comp.three_letter_code UMP _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 UMP N1 N1 N 0 1 N N N N N N 20.447 12.689 18.071 -2.460 0.157 -0.225 N1 UMP 1 UMP C2 C2 C 0 1 N N N N N N 20.926 11.704 17.241 -3.508 -0.069 -1.038 C2 UMP 2 UMP N3 N3 N 0 1 N N N N N N 20.589 10.398 17.525 -4.527 -0.860 -0.650 N3 UMP 3 UMP C4 C4 C 0 1 N N N N N N 19.824 10.026 18.595 -4.510 -1.441 0.567 C4 UMP 4 UMP C5 C5 C 0 1 N N N N N N 19.350 11.064 19.418 -3.413 -1.211 1.432 C5 UMP 5 UMP C6 C6 C 0 1 N N N N N N 19.707 12.367 19.148 -2.406 -0.414 1.018 C6 UMP 6 UMP O2 O2 O 0 1 N N N N N N 21.632 11.940 16.243 -3.536 0.448 -2.138 O2 UMP 7 UMP O4 O4 O 0 1 N N N N N N 19.562 8.808 18.746 -5.431 -2.156 0.919 O4 UMP 8 UMP "C1'" "C1'" C 0 1 N N R N N N 20.790 14.106 17.813 -1.364 1.017 -0.677 "C1'" UMP 9 UMP "C2'" "C2'" C 0 1 N N N N N N 19.576 14.957 17.530 -1.299 2.285 0.197 "C2'" UMP 10 UMP "C3'" "C3'" C 0 1 N N S N N N 19.269 15.668 18.818 0.127 2.258 0.798 "C3'" UMP 11 UMP "C4'" "C4'" C 0 1 N N R N N N 20.644 15.747 19.476 0.878 1.327 -0.187 "C4'" UMP 12 UMP "O3'" "O3'" O 0 1 N N N N N N 18.640 16.944 18.641 0.703 3.566 0.803 "O3'" UMP 13 UMP "O4'" "O4'" O 0 1 N N N N N N 21.395 14.611 19.000 -0.110 0.331 -0.528 "O4'" UMP 14 UMP "C5'" "C5'" C 0 1 N N N N N N 20.680 15.746 20.969 2.083 0.678 0.497 "C5'" UMP 15 UMP "O5'" "O5'" O 0 1 N N N N N N 20.080 14.578 21.461 2.823 -0.082 -0.461 "O5'" UMP 16 UMP P P P 0 1 N N N N N N 19.859 14.370 23.016 4.157 -0.901 -0.088 P UMP 17 UMP OP1 O1P O 0 1 N N N N N N 19.304 12.981 23.168 5.136 0.011 0.544 OP1 UMP 18 UMP OP2 O2P O 0 1 N N N N N N 21.183 14.526 23.710 3.790 -2.088 0.936 OP2 UMP 19 UMP OP3 O3P O 0 1 N Y N N N N 18.841 15.373 23.449 4.794 -1.527 -1.428 OP3 UMP 20 UMP HN3 HN3 H 0 1 N N N N N N 20.923 9.681 16.913 -5.275 -1.012 -1.248 HN3 UMP 21 UMP H5 H5 H 0 1 N N N N N N 18.709 10.840 20.258 -3.383 -1.668 2.410 H5 UMP 22 UMP H6 H6 H 0 1 N N N N N N 19.385 13.150 19.818 -1.561 -0.228 1.664 H6 UMP 23 UMP "H1'" "H1'" H 0 1 N N N N N N 21.488 14.172 16.965 -1.516 1.294 -1.720 "H1'" UMP 24 UMP "H2'" "H2'1" H 0 1 N N N N N N 19.794 15.683 16.733 -1.439 3.177 -0.414 "H2'" UMP 25 UMP "H2''" "H2'2" H 0 0 N N N N N N 18.727 14.326 17.228 -2.048 2.242 0.988 "H2''" UMP 26 UMP "H3'" "H3'" H 0 1 N N N N N N 18.626 15.021 19.433 0.118 1.835 1.803 "H3'" UMP 27 UMP "H4'" "H4'" H 0 1 N N N N N N 21.132 16.667 19.123 1.189 1.878 -1.074 "H4'" UMP 28 UMP "HO3'" "HO3'" H 0 0 N Y N N N N 18.475 17.337 19.490 0.215 4.209 1.335 "HO3'" UMP 29 UMP "H5'" "H5'1" H 0 1 N N N N N N 21.725 15.790 21.308 2.723 1.454 0.918 "H5'" UMP 30 UMP "H5''" "H5'2" H 0 0 N N N N N N 20.135 16.623 21.347 1.738 0.020 1.294 "H5''" UMP 31 UMP HOP2 HOP2 H 0 0 N N N N N N 21.424 13.704 24.121 3.152 -2.725 0.587 HOP2 UMP 32 UMP HOP3 HOP3 H 0 0 N N N N N N 18.053 14.924 23.731 5.603 -2.035 -1.279 HOP3 UMP 33 # 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 UMP N1 C2 SING N N 1 UMP N1 C6 SING N N 2 UMP N1 "C1'" SING N N 3 UMP C2 N3 SING N N 4 UMP C2 O2 DOUB N N 5 UMP N3 C4 SING N N 6 UMP N3 HN3 SING N N 7 UMP C4 C5 SING N N 8 UMP C4 O4 DOUB N N 9 UMP C5 C6 DOUB N N 10 UMP C5 H5 SING N N 11 UMP C6 H6 SING N N 12 UMP "C1'" "C2'" SING N N 13 UMP "C1'" "O4'" SING N N 14 UMP "C1'" "H1'" SING N N 15 UMP "C2'" "C3'" SING N N 16 UMP "C2'" "H2'" SING N N 17 UMP "C2'" "H2''" SING N N 18 UMP "C3'" "C4'" SING N N 19 UMP "C3'" "O3'" SING N N 20 UMP "C3'" "H3'" SING N N 21 UMP "C4'" "O4'" SING N N 22 UMP "C4'" "C5'" SING N N 23 UMP "C4'" "H4'" SING N N 24 UMP "O3'" "HO3'" SING N N 25 UMP "C5'" "O5'" SING N N 26 UMP "C5'" "H5'" SING N N 27 UMP "C5'" "H5''" SING N N 28 UMP "O5'" P SING N N 29 UMP P OP1 DOUB N N 30 UMP P OP2 SING N N 31 UMP P OP3 SING N N 32 UMP OP2 HOP2 SING N N 33 UMP OP3 HOP3 SING N N 34 # 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 UMP SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O" UMP InChI InChI 1.03 "InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" UMP InChIKey InChI 1.03 JSRLJPSBLDHEIO-SHYZEUOFSA-N UMP SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" UMP SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" UMP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" UMP SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)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 UMP "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5'-uridylic acid ; UMP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-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 UMP "Create component" 1999-07-08 RCSB UMP "Modify descriptor" 2011-06-04 RCSB UMP "Modify linking type" 2012-05-02 RCSB UMP "Modify synonyms" 2020-06-05 PDBE UMP "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UMP _pdbx_chem_comp_synonyms.name DUMP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id UMP _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C6 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #