data_7OK # _chem_comp.id 7OK _chem_comp.name "N-hydroxycytidine 5'-(dihydrogen phosphate) tautomer" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms "[(2R,3S,4R,5R)-5-[(4E)-4-hydroxyimino-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-08-11 _chem_comp.pdbx_modified_date 2021-08-13 _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 339.196 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 7OK _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 7OZU _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 7OK "O5'" O1 O 0 1 N N N 87.806 105.631 110.950 -3.051 0.301 -0.542 "O5'" 7OK 1 7OK "C5'" C1 C 0 1 N N N 87.538 106.577 109.878 -2.463 -0.679 0.317 "C5'" 7OK 2 7OK "C4'" C2 C 0 1 N N R 88.220 106.017 108.622 -1.340 -1.402 -0.429 "C4'" 7OK 3 7OK "O4'" O2 O 0 1 N N N 89.168 105.197 108.963 -0.264 -0.488 -0.698 "O4'" 7OK 4 7OK "C3'" C3 C 0 1 N N S 87.225 105.081 107.832 -0.771 -2.532 0.451 "C3'" 7OK 5 7OK "O3'" O3 O 0 1 N N N 86.306 105.787 107.066 -0.931 -3.797 -0.194 "O3'" 7OK 6 7OK "C2'" C4 C 0 1 N N R 88.185 104.268 106.997 0.730 -2.181 0.596 "C2'" 7OK 7 7OK "O2'" O4 O 0 1 N N N 88.652 105.039 105.910 1.540 -3.355 0.496 "O2'" 7OK 8 7OK "C1'" C5 C 0 1 N N R 89.198 104.016 107.846 0.963 -1.245 -0.617 "C1'" 7OK 9 7OK OAC O5 O 0 1 N N N 88.402 99.202 112.059 6.386 2.042 -0.404 OAC 7OK 10 7OK C5 C6 C 0 1 N N N 88.733 101.740 110.748 4.282 0.329 -0.949 C5 7OK 11 7OK P P1 P 0 1 N N N 87.689 106.155 112.547 -4.267 1.252 -0.085 P 7OK 12 7OK OP1 O6 O 0 1 N N N 86.670 107.457 112.645 -5.389 0.418 0.402 OP1 7OK 13 7OK OP3 O7 O 0 1 N Y N 87.153 104.906 113.507 -3.770 2.227 1.096 OP3 7OK 14 7OK N1 N1 N 0 1 N N N 89.215 102.813 108.721 2.102 -0.356 -0.371 N1 7OK 15 7OK C6 C7 C 0 1 N N N 88.716 102.872 109.956 3.225 -0.475 -1.156 C6 7OK 16 7OK C4 C8 C 0 1 N N N 89.276 100.574 110.213 4.205 1.323 0.132 C4 7OK 17 7OK N4 N2 N 0 1 N N N 89.314 99.374 111.007 5.207 2.124 0.376 N4 7OK 18 7OK N3 N3 N 0 1 N N N 89.758 100.571 108.975 3.039 1.389 0.888 N3 7OK 19 7OK C2 C9 C 0 1 N N N 89.730 101.671 108.229 2.021 0.552 0.614 C2 7OK 20 7OK O2 O8 O 0 1 N N N 90.163 101.650 107.130 1.005 0.616 1.280 O2 7OK 21 7OK OP2 O9 O 0 1 N N N 89.150 106.586 113.001 -4.759 2.134 -1.338 OP2 7OK 22 7OK "H5'" H1 H 0 1 N N N 87.955 107.564 110.129 -2.056 -0.189 1.201 "H5'" 7OK 23 7OK "H5''" H2 H 0 0 N N N 86.454 106.668 109.713 -3.222 -1.400 0.618 "H5''" 7OK 24 7OK "H4'" H3 H 0 1 N N N 88.550 106.839 107.970 -1.720 -1.813 -1.364 "H4'" 7OK 25 7OK "H3'" H4 H 0 1 N N N 86.719 104.422 108.552 -1.257 -2.538 1.426 "H3'" 7OK 26 7OK "HO3'" H5 H 0 0 N Y N 85.728 106.279 107.638 -0.590 -4.545 0.315 "HO3'" 7OK 27 7OK "H2'" H6 H 0 1 N N N 87.691 103.348 106.650 0.919 -1.659 1.533 "H2'" 7OK 28 7OK "HO2'" H7 H 0 0 N N N 89.255 104.521 105.390 1.366 -4.012 1.184 "HO2'" 7OK 29 7OK "H1'" H8 H 0 1 N N N 90.166 104.088 107.328 1.120 -1.825 -1.526 "H1'" 7OK 30 7OK H5 H10 H 0 1 N N N 88.337 101.759 111.753 5.168 0.244 -1.560 H5 7OK 31 7OK HOP3 H11 H 0 0 N Y N 86.350 105.164 113.945 -3.035 2.803 0.847 HOP3 7OK 32 7OK H6 H12 H 0 1 N N N 88.303 103.796 110.334 3.257 -1.217 -1.941 H6 7OK 33 7OK HOP2 H14 H 0 0 N N N 89.150 107.506 113.239 -5.491 2.732 -1.135 HOP2 7OK 34 7OK H2 H13 H 0 1 N N N 90.147 99.730 108.599 2.960 2.034 1.607 H2 7OK 35 7OK H1 H15 H 0 1 N N N 88.558 98.365 112.480 7.072 2.675 -0.149 H1 7OK 36 # # 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 7OK "O2'" "C2'" SING N N 1 7OK "C2'" "C3'" SING N N 2 7OK "C2'" "C1'" SING N N 3 7OK "O3'" "C3'" SING N N 4 7OK O2 C2 DOUB N N 5 7OK "C3'" "C4'" SING N N 6 7OK "C1'" N1 SING N N 7 7OK "C1'" "O4'" SING N N 8 7OK C2 N1 SING N N 9 7OK C2 N3 SING N N 10 7OK "C4'" "O4'" SING N N 11 7OK "C4'" "C5'" SING N N 12 7OK N1 C6 SING N N 13 7OK N3 C4 SING N N 14 7OK "C5'" "O5'" SING N N 15 7OK C6 C5 DOUB N N 16 7OK C4 C5 SING N N 17 7OK C4 N4 DOUB N E 18 7OK "O5'" P SING N N 19 7OK N4 OAC SING N N 20 7OK P OP1 DOUB N N 21 7OK P OP3 SING N N 22 7OK P OP2 SING N N 23 7OK "C5'" "H5'" SING N N 24 7OK "C5'" "H5''" SING N N 25 7OK "C4'" "H4'" SING N N 26 7OK "C3'" "H3'" SING N N 27 7OK "O3'" "HO3'" SING N N 28 7OK "C2'" "H2'" SING N N 29 7OK "O2'" "HO2'" SING N N 30 7OK "C1'" "H1'" SING N N 31 7OK C5 H5 SING N N 32 7OK OP3 HOP3 SING N N 33 7OK C6 H6 SING N N 34 7OK OP2 HOP2 SING N N 35 7OK N3 H2 SING N N 36 7OK OAC H1 SING N N 37 # # 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 7OK InChI InChI 1.03 "InChI=1S/C9H14N3O9P/c13-6-4(3-20-22(17,18)19)21-8(7(6)14)12-2-1-5(11-16)10-9(12)15/h1-2,4,6-8,13-14,16H,3H2,(H,10,11,15)(H2,17,18,19)/t4-,6-,7-,8-/m1/s1" 7OK InChIKey InChI 1.03 DYOUVDKCXLKHKY-XVFCMESISA-N 7OK SMILES_CANONICAL CACTVS 3.385 "O\N=C/1NC(=O)N(C=C/1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" 7OK SMILES CACTVS 3.385 "ON=C1NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" 7OK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C\1=CN(C(=O)N/C1=N/O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" 7OK SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=NO)C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id 7OK _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 7OK _pdbx_chem_comp_synonyms.name "[(2R,3S,4R,5R)-5-[(4E)-4-hydroxyimino-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 7OK "Create component" 2021-08-11 PDBE 7OK "Modify atom id" 2021-08-11 PDBE 7OK "Initial release" 2021-08-18 RCSB ##