data_6CN # _chem_comp.id 6CN _chem_comp.name ;6-cyanouridine 5'-phosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H12 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 349.191 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6CN _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 3EX1 _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 6CN O3P O3P O 0 1 N N N N N N 26.124 -10.312 12.834 -4.292 1.893 0.837 O1 6CN 1 6CN P P P 0 1 N N N N N N 25.210 -10.780 13.921 -4.432 0.940 -0.286 P1 6CN 2 6CN O1P O1P O 0 1 N N N N N N 25.766 -11.613 15.041 -5.597 -0.119 0.051 O2 6CN 3 6CN O2P O2P O 0 1 N N N N N N 23.895 -11.328 13.430 -4.811 1.744 -1.629 O3 6CN 4 6CN "O5'" "O5'" O 0 1 N N N N N N 24.853 -9.424 14.716 -3.042 0.157 -0.503 O4 6CN 5 6CN "C5'" "C5'" C 0 1 N N N N N N 24.044 -8.359 14.163 -2.385 -0.565 0.539 C1 6CN 6 6CN "C4'" "C4'" C 0 1 N N R N N N 24.127 -7.189 15.140 -1.096 -1.185 -0.004 C2 6CN 7 6CN "C3'" "C3'" C 0 1 N N S N N N 23.347 -7.486 16.415 -0.432 -2.074 1.071 C3 6CN 8 6CN "O3'" "O3'" O 0 1 N N N N N N 23.988 -6.836 17.572 -0.756 -3.448 0.854 O5 6CN 9 6CN "C2'" "C2'" C 0 1 N N R N N N 21.966 -6.952 16.123 1.082 -1.837 0.872 C4 6CN 10 6CN "O2'" "O2'" O 0 1 N N N N N N 21.341 -6.512 17.332 1.739 -3.058 0.525 O6 6CN 11 6CN "O4'" "O4'" O 0 1 N N N N N N 23.526 -6.057 14.505 -0.122 -0.156 -0.284 O7 6CN 12 6CN "C1'" "C1'" C 0 1 N N R N N N 22.259 -5.801 15.160 1.154 -0.833 -0.300 C5 6CN 13 6CN N1 N1 N 0 1 N N N N N N 21.224 -5.467 14.133 2.242 0.124 -0.086 N1 6CN 14 6CN C6 C6 C 0 1 N N N N N N 20.662 -4.271 14.131 3.287 0.184 -0.983 C6 6CN 15 6CN C5 C5 C 0 1 N N N N N N 19.583 -4.104 13.317 4.295 1.077 -0.777 C7 6CN 16 6CN C4 C4 C 0 1 N N N N N N 19.450 -4.867 12.204 4.241 1.923 0.360 C8 6CN 17 6CN O4 O4 O 0 1 N N N N N N 18.612 -4.531 11.348 5.128 2.730 0.567 O8 6CN 18 6CN N3 N3 N 0 1 N N N N N N 19.992 -6.044 12.218 3.198 1.827 1.208 N2 6CN 19 6CN C2 C2 C 0 1 N N N N N N 20.874 -6.397 13.162 2.211 0.942 0.982 C9 6CN 20 6CN O2 O2 O 0 1 N N N N N N 21.361 -7.529 13.140 1.280 0.873 1.761 O9 6CN 21 6CN C7 C7 C 0 1 N N N N N N 21.639 -3.314 13.880 3.313 -0.684 -2.121 C10 6CN 22 6CN N8 N8 N 0 1 N N N N N N 22.433 -2.537 13.677 3.334 -1.374 -3.024 N3 6CN 23 6CN HO1P HO1P H 0 0 N N N N N N 25.883 -12.507 14.743 -5.745 -0.776 -0.643 H1 6CN 24 6CN HO2P HO2P H 0 0 N N N N N N 23.305 -11.443 14.166 -5.639 2.240 -1.570 H2 6CN 25 6CN "H5'" "H5'" H 0 1 N N N N N N 24.426 -8.061 13.175 -2.144 0.115 1.357 H3 6CN 26 6CN "H5'A" "H5'A" H 0 0 N N N N N N 23.002 -8.686 14.028 -3.042 -1.354 0.905 H4 6CN 27 6CN "H4'" "H4'" H 0 1 N N N N N N 25.179 -7.008 15.404 -1.304 -1.767 -0.901 H5 6CN 28 6CN "H3'" "H3'" H 0 1 N N N N N N 23.313 -8.553 16.679 -0.741 -1.762 2.069 H6 6CN 29 6CN "HO3'" "HO3'" H 0 0 N N N N N N 24.126 -7.477 18.260 -0.365 -4.052 1.501 H7 6CN 30 6CN "H2'" "H2'" H 0 1 N N N N N N 21.268 -7.688 15.697 1.523 -1.409 1.772 H8 6CN 31 6CN "HO2'" "HO2'" H 0 0 N N N N N N 21.998 -6.414 18.011 1.673 -3.746 1.202 H9 6CN 32 6CN "H1'" "H1'" H 0 1 N N N N N N 22.271 -4.909 15.803 1.291 -1.360 -1.244 H10 6CN 33 6CN H5 H5 H 0 1 N N N N N N 18.834 -3.364 13.558 5.123 1.139 -1.468 H11 6CN 34 6CN HN3 HN3 H 0 1 N N N N N N 19.746 -6.704 11.508 3.157 2.404 1.987 H12 6CN 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 6CN O3P P DOUB N N 1 6CN P "O5'" SING N N 2 6CN P O1P SING N N 3 6CN O1P HO1P SING N N 4 6CN O2P P SING N N 5 6CN O2P HO2P SING N N 6 6CN "C5'" "O5'" SING N N 7 6CN "C5'" "C4'" SING N N 8 6CN "C5'" "H5'" SING N N 9 6CN "C5'" "H5'A" SING N N 10 6CN "C4'" "C3'" SING N N 11 6CN "C4'" "H4'" SING N N 12 6CN "C3'" "O3'" SING N N 13 6CN "C3'" "H3'" SING N N 14 6CN "O3'" "HO3'" SING N N 15 6CN "C2'" "C3'" SING N N 16 6CN "C2'" "O2'" SING N N 17 6CN "C2'" "H2'" SING N N 18 6CN "O2'" "HO2'" SING N N 19 6CN "O4'" "C4'" SING N N 20 6CN "O4'" "C1'" SING N N 21 6CN "C1'" "C2'" SING N N 22 6CN "C1'" "H1'" SING N N 23 6CN N1 "C1'" SING N N 24 6CN C6 N1 SING N N 25 6CN C5 C6 DOUB N N 26 6CN C5 H5 SING N N 27 6CN C4 C5 SING N N 28 6CN C4 N3 SING N N 29 6CN O4 C4 DOUB N N 30 6CN N3 C2 SING N N 31 6CN N3 HN3 SING N N 32 6CN C2 N1 SING N N 33 6CN O2 C2 DOUB N N 34 6CN C7 C6 SING N N 35 6CN N8 C7 TRIP 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 6CN SMILES ACDLabs 10.04 "N#CC=1N(C(=O)NC(=O)C=1)C2OC(C(O)C2O)COP(=O)(O)O" 6CN 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" 6CN SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)C=C2C#N" 6CN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C#N" 6CN SMILES "OpenEye OEToolkits" 1.5.0 "C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)C#N" 6CN InChI InChI 1.03 "InChI=1S/C10H12N3O9P/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/h1,5,7-9,15-16H,3H2,(H,12,14,17)(H2,18,19,20)/t5-,7-,8-,9-/m1/s1" 6CN InChIKey InChI 1.03 GCVKNFUDFHDSJQ-ZOQUXTDFSA-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 6CN "SYSTEMATIC NAME" ACDLabs 10.04 ;6-cyanouridine 5'-(dihydrogen phosphate) ; 6CN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-cyano-2,4-dioxo-pyrimidin-1-yl)-3,4-dihydroxy-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 6CN "Create component" 2008-10-23 RCSB 6CN "Modify descriptor" 2011-06-04 RCSB 6CN "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 6CN _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 C6 _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 ? #