data_16B # _chem_comp.id 16B _chem_comp.name "N-hydroxycytidine 5'-(dihydrogen phosphate)" _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 ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-10-18 _chem_comp.pdbx_modified_date 2021-08-11 _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 16B _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 4HIB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 16B OP1 OAA O 0 1 N N N 3.588 14.113 29.523 3.702 -2.145 1.092 OP1 16B 1 16B P PAE P 0 1 N N N 3.724 13.339 30.931 4.165 -1.339 -0.060 P 16B 2 16B OP3 OAD O 0 1 N Y N 2.220 12.934 31.347 5.481 -0.512 0.359 OP3 16B 3 16B OP2 OAF O 0 1 N N N 4.472 14.140 31.917 4.515 -2.316 -1.291 OP2 16B 4 16B "O5'" "O5'" O 0 1 N N N 4.469 11.891 30.758 3.004 -0.315 -0.500 "O5'" 16B 5 16B "C5'" "C5'" C 0 1 N N N 4.217 10.720 29.889 2.401 0.613 0.405 "C5'" 16B 6 16B "C4'" "C4'" C 0 1 N N R 5.326 9.545 30.128 1.341 1.431 -0.336 "C4'" 16B 7 16B "O4'" "O4'" O 0 1 N N N 4.870 8.414 29.238 0.252 0.579 -0.728 "O4'" 16B 8 16B "C3'" "C3'" C 0 1 N N S 6.858 9.763 29.754 0.766 2.513 0.599 "C3'" 16B 9 16B "O3'" "O3'" O 0 1 N N N 7.839 9.173 30.669 0.998 3.815 0.059 "O3'" 16B 10 16B "C2'" "C2'" C 0 1 N N R 7.014 9.124 28.373 -0.751 2.207 0.645 "C2'" 16B 11 16B "O2'" "O2'" O 0 1 N N N 8.446 8.876 28.091 -1.517 3.413 0.598 "O2'" 16B 12 16B "C1'" "C1'" C 0 1 N N R 6.100 7.872 28.503 -0.953 1.370 -0.648 "C1'" 16B 13 16B N1 NAM N 0 1 N N N 5.695 7.281 27.175 -2.132 0.509 -0.526 N1 16B 14 16B C2 CAL C 0 1 N N N 4.969 6.105 27.001 -2.146 -0.480 0.387 C2 16B 15 16B O2 OAK O 0 1 N N N 4.654 5.430 27.964 -1.175 -0.647 1.106 O2 16B 16 16B N3 NAG N 0 1 N N N 4.621 5.685 25.761 -3.204 -1.277 0.520 N3 16B 17 16B C6 CAN C 0 1 N N N 6.017 8.059 26.053 -3.209 0.715 -1.334 C6 16B 18 16B C5 CAI C 0 1 N N N 5.654 7.627 24.793 -4.293 -0.088 -1.211 C5 16B 19 16B C4 CAH C 0 1 N N N 4.962 6.426 24.673 -4.274 -1.117 -0.248 C4 16B 20 16B N4 NAB N 0 1 N N N 4.624 6.111 23.454 -5.361 -1.948 -0.102 N4 16B 21 16B OAC OAC O 0 1 N N N 3.722 7.036 22.967 -5.338 -2.980 0.867 OAC 16B 22 16B HOP3 H1 H 0 0 N Y N 1.614 13.238 30.681 5.841 0.039 -0.349 HOP3 16B 23 16B HOP2 H2 H 0 0 N N N 4.730 14.966 31.524 5.208 -2.962 -1.097 HOP2 16B 24 16B "H5'" H3 H 0 1 N N N 4.257 11.040 28.837 1.932 0.068 1.224 "H5'" 16B 25 16B "H5''" H4 H 0 0 N N N 3.218 10.318 30.112 3.164 1.281 0.802 "H5''" 16B 26 16B "H4'" H5 H 0 1 N N N 5.266 9.231 31.180 1.782 1.898 -1.216 "H4'" 16B 27 16B "H3'" H6 H 0 1 N N N 7.037 10.845 29.667 1.205 2.429 1.594 "H3'" 16B 28 16B "HO3'" H7 H 0 0 N Y N 7.747 9.566 31.529 0.657 4.535 0.608 "HO3'" 16B 29 16B "H2'" H8 H 0 1 N N N 6.592 9.797 27.612 -1.003 1.623 1.530 "H2'" 16B 30 16B "HO2'" H9 H 0 0 N N N 8.906 9.705 28.033 -1.424 3.970 1.383 "HO2'" 16B 31 16B "H1'" H10 H 0 1 N N N 6.601 7.112 29.121 -1.041 2.022 -1.517 "H1'" 16B 32 16B H6 H11 H 0 1 N N N 6.547 8.992 26.174 -3.199 1.511 -2.064 H6 16B 33 16B H5 H12 H 0 1 N N N 5.902 8.210 23.918 -5.158 0.059 -1.841 H5 16B 34 16B H41 H13 H 0 1 N N N 4.966 5.319 22.948 -6.143 -1.826 -0.663 H41 16B 35 16B H14 H14 H 0 1 N N N 3.478 6.804 22.079 -6.146 -3.511 0.895 H14 16B 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 16B OAC N4 SING N N 1 16B N4 C4 SING N N 2 16B C4 C5 SING N N 3 16B C4 N3 DOUB N N 4 16B C5 C6 DOUB N N 5 16B N3 C2 SING N N 6 16B C6 N1 SING N N 7 16B C2 N1 SING N N 8 16B C2 O2 DOUB N N 9 16B N1 "C1'" SING N N 10 16B "O2'" "C2'" SING N N 11 16B "C2'" "C1'" SING N N 12 16B "C2'" "C3'" SING N N 13 16B "C1'" "O4'" SING N N 14 16B "O4'" "C4'" SING N N 15 16B OP1 P DOUB N N 16 16B "C3'" "C4'" SING N N 17 16B "C3'" "O3'" SING N N 18 16B "C5'" "C4'" SING N N 19 16B "C5'" "O5'" SING N N 20 16B "O5'" P SING N N 21 16B P OP3 SING N N 22 16B P OP2 SING N N 23 16B OP3 HOP3 SING N N 24 16B OP2 HOP2 SING N N 25 16B "C5'" "H5'" SING N N 26 16B "C5'" "H5''" SING N N 27 16B "C4'" "H4'" SING N N 28 16B "C3'" "H3'" SING N N 29 16B "O3'" "HO3'" SING N N 30 16B "C2'" "H2'" SING N N 31 16B "O2'" "HO2'" SING N N 32 16B "C1'" "H1'" SING N N 33 16B C6 H6 SING N N 34 16B C5 H5 SING N N 35 16B N4 H41 SING N N 36 16B OAC H14 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 16B SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(N2C=CC(=NC2=O)NO)C(O)C1O" 16B 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" 16B InChIKey InChI 1.03 DYOUVDKCXLKHKY-XVFCMESISA-N 16B SMILES_CANONICAL CACTVS 3.385 "ONC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" 16B SMILES CACTVS 3.385 "ONC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" 16B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1NO)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" 16B SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1NO)C2C(C(C(O2)COP(=O)(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 16B "SYSTEMATIC NAME" ACDLabs 12.01 "N-hydroxycytidine 5'-(dihydrogen phosphate)" 16B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[4-(oxidanylamino)-2-oxidanylidene-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 16B "Create component" 2012-10-18 RCSB 16B "Initial release" 2012-11-09 RCSB 16B "Modify atom id" 2021-07-27 RCSB 16B "Modify atom id" 2021-08-11 PDBE ##