data_UMC # _chem_comp.id UMC _chem_comp.name ;2'-deoxy-5'-uridylic acid ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-08-03 _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 310.198 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UMC _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 UMC P P P 0 1 N N N N N N 111.030 23.670 31.307 4.002 -0.968 -0.034 P UMC 1 UMC N1 N1 N 0 1 N N N N N N 108.555 19.926 26.633 -2.553 0.335 -0.543 N1 UMC 2 UMC C2 C2 C 0 1 N N N N N N 107.749 19.850 25.576 -2.582 -0.159 0.706 C2 UMC 3 UMC O2 O2 O 0 1 N N N N N N 107.922 20.574 24.590 -1.701 0.147 1.485 O2 UMC 4 UMC N3 N3 N 0 1 N N N N N N 106.746 18.957 25.611 -3.562 -0.981 1.115 N3 UMC 5 UMC C4 C4 C 0 1 N N N N N N 106.589 18.026 26.567 -4.416 -1.533 0.233 C4 UMC 6 UMC O4 O4 O 0 1 N N N N N N 105.668 17.202 26.485 -5.343 -2.208 0.628 O4 UMC 7 UMC C5 C5 C 0 1 N N N N N N 107.565 17.951 27.714 -4.220 -1.311 -1.245 C5 UMC 8 UMC C6 C6 C 0 1 N N N N N N 108.334 19.248 27.911 -3.658 0.094 -1.473 C6 UMC 9 UMC "C1'" C1* C 0 1 N N R N N N 109.753 20.776 26.582 -1.403 1.131 -0.978 C1* UMC 10 UMC O1P O1P O 0 1 N N N N N N 112.246 24.415 31.810 3.539 -2.091 1.023 O1P UMC 11 UMC "C2'" C2* C 0 1 N N N N N N 109.530 22.263 26.854 -1.328 2.435 -0.160 C2* UMC 12 UMC O2P O2P O 0 1 N N N N N N 110.124 24.517 30.462 4.986 -0.065 0.605 O2P UMC 13 UMC "C3'" C3* C 0 1 N N S N N N 110.919 22.693 27.302 0.065 2.382 0.512 C3* UMC 14 UMC "O3'" O3* O 0 1 N N N N N N 111.800 22.856 26.183 0.693 3.665 0.488 O3* UMC 15 UMC O3P O3P O 0 1 N N N N N N 110.308 22.861 32.378 4.676 -1.679 -1.311 O3P UMC 16 UMC "C4'" C4* C 0 1 N N R N N N 111.369 21.509 28.135 0.824 1.377 -0.393 C4* UMC 17 UMC "O4'" O4* O 0 1 N N N N N N 110.714 20.374 27.562 -0.186 0.405 -0.737 O4* UMC 18 UMC "C5'" C5* C 0 1 N N N N N N 110.906 21.645 29.576 1.968 0.715 0.378 C5* UMC 19 UMC "O5'" O5* O 0 1 N N N N N N 111.701 22.590 30.300 2.721 -0.116 -0.508 O5* UMC 20 UMC H6 H6 H 0 1 N N N N N N 109.307 19.023 28.372 -4.443 0.831 -1.304 H6 UMC 21 UMC "H2'" H2* H 0 1 N N N N N N 108.784 22.420 27.647 -1.403 3.302 -0.816 H2* UMC 22 UMC "H5'" H5* H 0 1 N N N N N N 109.858 21.980 29.584 2.618 1.485 0.795 H5* UMC 23 UMC "H2'A" H2*A H 0 0 N N N N N N 109.217 22.797 25.945 -2.115 2.457 0.595 H2*A UMC 24 UMC "H5'A" H5*A H 0 0 N N N N N N 110.981 20.664 30.069 1.559 0.109 1.186 H5*A UMC 25 UMC "H1'" H1* H 0 1 N N N N N N 110.202 20.683 25.582 -1.494 1.365 -2.039 H1* UMC 26 UMC "H3'" H3* H 0 1 N N N N N N 110.863 23.603 27.918 -0.009 2.006 1.533 H3* UMC 27 UMC "HO3'" HO3* H 0 0 N N N N N N 112.658 23.124 26.491 0.206 4.350 0.966 HO3* UMC 28 UMC "H4'" H4* H 0 1 N N N N N N 112.464 21.408 28.095 1.202 1.875 -1.286 H4* UMC 29 UMC H5 H5 H 0 1 N N N N N N 108.283 17.142 27.514 -3.521 -2.051 -1.635 H5 UMC 30 UMC H5A H5A H 0 1 N N N N N N 107.009 17.727 28.636 -5.177 -1.408 -1.758 H5A UMC 31 UMC HN3 HN3 H 0 1 N N N N N N 106.070 18.987 24.875 -3.656 -1.181 2.059 HN3 UMC 32 UMC H6A H6A H 0 1 N N N N N N 107.759 19.910 28.575 -3.295 0.179 -2.497 H6A UMC 33 UMC HO1P HO1P H 0 0 N N N N N N 112.222 25.311 31.495 2.893 -2.719 0.672 HO1P UMC 34 UMC HO3P HO3P H 0 0 N N N N N N 109.375 23.033 32.330 5.456 -2.210 -1.100 HO3P UMC 35 # 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 UMC "O5'" P SING N N 1 UMC O2P P DOUB N N 2 UMC P O1P SING N N 3 UMC P O3P SING N N 4 UMC C2 N1 SING N N 5 UMC "C1'" N1 SING N N 6 UMC N1 C6 SING N N 7 UMC O2 C2 DOUB N N 8 UMC C2 N3 SING N N 9 UMC HN3 N3 SING N N 10 UMC N3 C4 SING N N 11 UMC O4 C4 DOUB N N 12 UMC C4 C5 SING N N 13 UMC H5A C5 SING N N 14 UMC C5 C6 SING N N 15 UMC C5 H5 SING N N 16 UMC C6 H6 SING N N 17 UMC C6 H6A SING N N 18 UMC "H1'" "C1'" SING N N 19 UMC "C1'" "C2'" SING N N 20 UMC "C1'" "O4'" SING N N 21 UMC O1P HO1P SING N N 22 UMC "H2'A" "C2'" SING N N 23 UMC "C2'" "C3'" SING N N 24 UMC "C2'" "H2'" SING N N 25 UMC "O3'" "C3'" SING N N 26 UMC "C3'" "H3'" SING N N 27 UMC "C3'" "C4'" SING N N 28 UMC "HO3'" "O3'" SING N N 29 UMC O3P HO3P SING N N 30 UMC "O4'" "C4'" SING N N 31 UMC "H4'" "C4'" SING N N 32 UMC "C4'" "C5'" SING N N 33 UMC "C5'" "H5'" SING N N 34 UMC "C5'" "H5'A" SING N N 35 UMC "C5'" "O5'" SING N N 36 # 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 UMC SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)CC1)CC2O" UMC InChI InChI 1.03 "InChI=1S/C9H15N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h5-6,8,12H,1-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" UMC InChIKey InChI 1.03 WQQZADPPRABIFU-SHYZEUOFSA-N UMC SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O" UMC SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O" UMC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" UMC SMILES "OpenEye OEToolkits" 1.7.6 "C1CN(C(=O)NC1=O)C2CC(C(O2)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 UMC "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5'-uridylic acid ; UMC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-1,3-diazinan-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 UMC "Create component" 2012-08-03 RCSB UMC "Other modification" 2012-08-07 RCSB UMC "Initial release" 2012-08-24 RCSB UMC "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id UMC _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 ? #