data_U1P # _chem_comp.id U1P _chem_comp.name ;6-[(E)-iminomethyl]uridine 5'-phosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-10-23 _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 351.207 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U1P _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 3EWW _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 U1P O1P O1P O 0 1 N N N N N N 26.340 -9.975 12.799 -4.377 1.855 0.803 O1P U1P 1 U1P P P P 0 1 N N N N N N 25.301 -10.258 13.859 -4.496 0.919 -0.338 P U1P 2 U1P O2P O2P O 0 1 N N N N N N 23.995 -10.769 13.287 -5.662 -0.149 -0.036 O2P U1P 3 U1P O3P O3P O 0 1 N N N N N N 25.838 -11.079 14.948 -4.855 1.743 -1.673 O3P U1P 4 U1P N1 N1 N 0 1 N N N N N N 21.281 -4.950 14.005 2.177 0.123 -0.039 N1 U1P 5 U1P C2 C2 C 0 1 N N N N N N 20.848 -5.901 13.074 2.091 0.973 0.999 C2 U1P 6 U1P O2 O2 O 0 1 N N N N N N 21.427 -7.009 13.099 1.113 0.937 1.722 O2 U1P 7 U1P N3 N3 N 0 1 N N N N N N 19.939 -5.649 12.118 3.068 1.863 1.253 N3 U1P 8 U1P C4 C4 C 0 1 N N N N N N 19.331 -4.453 12.101 4.161 1.922 0.467 C4 U1P 9 U1P O4 O4 O 0 1 N N N N N N 18.520 -4.270 11.198 5.042 2.729 0.701 O4 U1P 10 U1P C6 C6 C 0 1 N N N N N N 20.665 -3.717 13.956 3.279 0.141 -0.869 C6 U1P 11 U1P C5 C5 C 0 1 N N N N N N 19.703 -3.470 12.983 4.277 1.037 -0.635 C5 U1P 12 U1P "O5'" O5* O 0 1 N N N N N N 25.008 -8.844 14.607 -3.099 0.145 -0.544 O5* U1P 13 U1P "C5'" C5* C 0 1 N N N N N N 24.379 -7.738 13.916 -2.456 -0.592 0.498 C5* U1P 14 U1P "C4'" C4* C 0 1 N N R N N N 24.068 -6.755 15.043 -1.156 -1.199 -0.034 C4* U1P 15 U1P "C3'" C3* C 0 1 N N S N N N 23.012 -7.404 15.880 -0.507 -2.103 1.038 C3* U1P 16 U1P "O3'" O3* O 0 1 N N N N N N 23.460 -7.758 17.185 -0.823 -3.475 0.794 O3* U1P 17 U1P "C2'" C2* C 0 1 N N R N N N 21.809 -6.483 15.911 1.009 -1.857 0.868 C2* U1P 18 U1P "O2'" O2* O 0 1 N N N N N N 21.482 -6.129 17.238 1.675 -3.071 0.513 O2* U1P 19 U1P "O4'" O4* O 0 1 N N N N N N 23.499 -5.577 14.455 -0.182 -0.162 -0.281 O4* U1P 20 U1P "C1'" C1* C 0 1 N N R N N N 22.241 -5.262 15.078 1.096 -0.835 -0.287 C1* U1P 21 U1P C7 C7 C 0 1 N N N N N N 21.098 -2.678 14.797 3.372 -0.798 -2.004 C7 U1P 22 U1P N8 N8 N 0 1 N N N N N N 22.365 -2.247 14.624 4.447 -0.844 -2.718 N8 U1P 23 U1P HO2P HO2P H 0 0 N N N N N N 23.362 -10.876 13.988 -5.796 -0.795 -0.743 HO2P U1P 24 U1P HO3P HO3P H 0 0 N N N N N N 25.954 -11.972 14.645 -5.686 2.236 -1.620 HO3P U1P 25 U1P HN3 HN3 H 0 1 N N N N N N 19.719 -6.341 11.430 2.984 2.467 2.007 HN3 U1P 26 U1P H5 H5 H 0 1 N N N N N N 19.244 -2.494 12.921 5.146 1.070 -1.276 H5 U1P 27 U1P "H5'" H5* H 0 1 N N N N N N 25.050 -7.295 13.165 -2.232 0.076 1.330 H5* U1P 28 U1P "H5'A" H5*A H 0 0 N N N N N N 23.485 -8.038 13.350 -3.116 -1.389 0.840 H5*A U1P 29 U1P "H4'" H4* H 0 1 N N N N N N 24.963 -6.500 15.629 -1.348 -1.767 -0.944 H4* U1P 30 U1P "H3'" H3* H 0 1 N N N N N N 22.737 -8.366 15.423 -0.832 -1.806 2.035 H3* U1P 31 U1P "HO3'" HO3* H 0 0 N Y N N N N 24.407 -7.837 17.185 -0.441 -4.087 1.437 HO3* U1P 32 U1P "H2'" H2* H 0 1 N N N N N N 20.902 -6.952 15.503 1.434 -1.442 1.781 H2* U1P 33 U1P "HO2'" HO2* H 0 0 N N N N N N 21.409 -6.915 17.767 1.600 -3.769 1.177 HO2* U1P 34 U1P "H1'" H1* H 0 1 N N N N N N 22.304 -4.394 15.751 1.252 -1.345 -1.237 H1* U1P 35 U1P H7 H7 H 0 1 N N N N N N 20.449 -2.246 15.545 2.541 -1.448 -2.237 H7 U1P 36 U1P HN8 HN8 H 0 1 N N N N N N 22.548 -1.513 15.278 4.508 -1.461 -3.464 HN8 U1P 37 # 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 U1P O1P P DOUB N N 1 U1P O2P P SING N N 2 U1P P "O5'" SING N N 3 U1P P O3P SING N N 4 U1P O2P HO2P SING N N 5 U1P O3P HO3P SING N N 6 U1P C2 N1 SING N N 7 U1P C6 N1 SING N N 8 U1P N1 "C1'" SING N N 9 U1P N3 C2 SING N N 10 U1P C2 O2 DOUB N N 11 U1P C4 N3 SING N N 12 U1P N3 HN3 SING N N 13 U1P O4 C4 DOUB N N 14 U1P C4 C5 SING N N 15 U1P C5 C6 DOUB N N 16 U1P C6 C7 SING N N 17 U1P C5 H5 SING N N 18 U1P "C5'" "O5'" SING N N 19 U1P "C5'" "C4'" SING N N 20 U1P "C5'" "H5'" SING N N 21 U1P "C5'" "H5'A" SING N N 22 U1P "O4'" "C4'" SING N N 23 U1P "C4'" "C3'" SING N N 24 U1P "C4'" "H4'" SING N N 25 U1P "C3'" "C2'" SING N N 26 U1P "C3'" "O3'" SING N N 27 U1P "C3'" "H3'" SING N N 28 U1P "O3'" "HO3'" SING N N 29 U1P "C1'" "C2'" SING N N 30 U1P "C2'" "O2'" SING N N 31 U1P "C2'" "H2'" SING N N 32 U1P "O2'" "HO2'" SING N N 33 U1P "O4'" "C1'" SING N N 34 U1P "C1'" "H1'" SING N N 35 U1P N8 C7 DOUB N N 36 U1P C7 H7 SING N N 37 U1P N8 HN8 SING N N 38 # 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 U1P SMILES ACDLabs 10.04 "O=C1NC(=O)N(C(C=[N@H])=C1)C2OC(C(O)C2O)COP(=O)(O)O" U1P SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2C=N" U1P SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2C=N" U1P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[H]/N=C/C1=CC(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" U1P SMILES "OpenEye OEToolkits" 1.5.0 "[H]N=CC1=CC(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O" U1P InChI InChI 1.03 "InChI=1S/C10H14N3O9P/c11-2-4-1-6(14)12-10(17)13(4)9-8(16)7(15)5(22-9)3-21-23(18,19)20/h1-2,5,7-9,11,15-16H,3H2,(H,12,14,17)(H2,18,19,20)/b11-2+/t5-,7-,8-,9-/m1/s1" U1P InChIKey InChI 1.03 GSNYQYNODBCZBM-XDMCGQROSA-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 U1P "SYSTEMATIC NAME" ACDLabs 10.04 ;6-[(E)-iminomethyl]uridine 5'-(dihydrogen phosphate) ; U1P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-[6-(iminomethyl)-2,4-dioxo-pyrimidin-1-yl]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 U1P "Create component" 2008-10-23 RCSB U1P "Modify descriptor" 2011-06-04 RCSB U1P "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id U1P _pdbx_chem_comp_pcm.modified_residue_id LYS _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 C7 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #