data_8YN # _chem_comp.id 8YN _chem_comp.name Pseudoisocytidine _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-03-27 _chem_comp.pdbx_modified_date 2019-05-07 _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 307.197 _chem_comp.one_letter_code C _chem_comp.three_letter_code 8YN _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 5NIP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 8YN P P1 P 0 1 N N N 26.249 26.755 11.852 -3.932 1.021 -0.110 P 8YN 1 8YN C1 C1 C 0 1 N N N 20.568 24.914 11.401 2.516 -0.359 -0.375 C1 8YN 2 8YN C2 C2 C 0 1 N N N 19.967 23.661 11.714 2.484 0.606 0.646 C2 8YN 3 8YN C4 C3 C 0 1 N N N 18.991 24.540 13.674 4.585 1.353 -0.078 C4 8YN 4 8YN C6 C4 C 0 1 N N N 20.338 25.986 12.308 3.602 -0.410 -1.201 C6 8YN 5 8YN O1P O1 O 0 1 N N N 27.687 26.416 11.788 -4.469 1.803 -1.411 O1P 8YN 6 8YN O2P O2 O 0 1 N N N 25.834 28.155 12.065 -5.019 0.184 0.446 O2P 8YN 7 8YN "O5'" O3 O 0 1 N N N 25.620 26.227 10.460 -2.690 0.084 -0.522 "O5'" 8YN 8 8YN "C5'" C5 C 0 1 N N N 24.494 26.866 9.861 -2.058 -0.817 0.390 "C5'" 8YN 9 8YN "C4'" C6 C 0 1 N N R 23.448 25.851 9.387 -0.919 -1.549 -0.322 "C4'" 8YN 10 8YN "O4'" O4 O 0 1 N N N 22.776 25.296 10.517 0.121 -0.618 -0.665 "O4'" 8YN 11 8YN "C1'" C7 C 0 1 N N R 21.425 25.101 10.159 1.374 -1.327 -0.552 "C1'" 8YN 12 8YN O2 O5 O 0 1 N N N 20.135 22.719 10.939 1.529 0.679 1.403 O2 8YN 13 8YN N3 N1 N 0 1 N N N 19.233 23.487 12.855 3.529 1.450 0.775 N3 8YN 14 8YN N4 N2 N 0 1 N N N 18.179 24.330 14.668 5.641 2.213 0.059 N4 8YN 15 8YN N5 N3 N 0 1 N N N 19.521 25.780 13.423 4.608 0.445 -1.033 N5 8YN 16 8YN "C2'" C8 C 0 1 N N N 21.142 26.391 9.390 1.188 -2.190 0.722 "C2'" 8YN 17 8YN "C3'" C9 C 0 1 N N S 22.366 26.472 8.490 -0.302 -2.600 0.621 "C3'" 8YN 18 8YN "O3'" O6 O 0 1 N N N 22.215 25.665 7.331 -0.423 -3.908 0.060 "O3'" 8YN 19 8YN H6 H1 H 0 1 N N N 20.791 26.951 12.136 3.644 -1.144 -1.991 H6 8YN 20 8YN H1 H2 H 0 1 N N N 28.204 27.205 11.901 -5.219 2.388 -1.237 H1 8YN 21 8YN "H52'" H4 H 0 0 N N N 24.837 27.454 8.997 -1.658 -0.257 1.235 "H52'" 8YN 22 8YN "H51'" H5 H 0 0 N N N 24.030 27.536 10.600 -2.789 -1.542 0.749 "H51'" 8YN 23 8YN "H4'" H6 H 0 1 N N N 23.959 25.057 8.823 -1.296 -2.033 -1.223 "H4'" 8YN 24 8YN "H1'" H7 H 0 1 N N N 21.307 24.236 9.490 1.539 -1.958 -1.426 "H1'" 8YN 25 8YN H3 H8 H 0 1 N N N 18.875 22.582 13.085 3.528 2.124 1.473 H3 8YN 26 8YN H41 H9 H 0 1 N N N 17.925 25.084 15.274 5.633 2.884 0.759 H41 8YN 27 8YN H42 H10 H 0 1 N N N 17.808 23.415 14.826 6.398 2.151 -0.545 H42 8YN 28 8YN "H22'" H11 H 0 0 N N N 21.080 27.257 10.065 1.835 -3.066 0.696 "H22'" 8YN 29 8YN "H21'" H12 H 0 0 N N N 20.214 26.316 8.803 1.370 -1.601 1.621 "H21'" 8YN 30 8YN "H3'" H13 H 0 1 N N N 22.610 27.517 8.249 -0.776 -2.559 1.601 "H3'" 8YN 31 8YN H4 H14 H 0 1 N N N 21.548 26.040 6.768 -0.051 -4.609 0.612 H4 8YN 32 8YN O3P O3P O 0 1 N Y N 25.580 25.829 12.976 -3.456 2.088 0.998 O3P 8YN 33 8YN H2 H15 H 0 1 N Y N 25.050 26.365 13.555 -2.744 2.671 0.702 H2 8YN 34 # # 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 8YN "O3'" "C3'" SING N N 1 8YN "C3'" "C4'" SING N N 2 8YN "C3'" "C2'" SING N N 3 8YN "C4'" "C5'" SING N N 4 8YN "C4'" "O4'" SING N N 5 8YN "C2'" "C1'" SING N N 6 8YN "C5'" "O5'" SING N N 7 8YN "C1'" "O4'" SING N N 8 8YN "C1'" C1 SING N N 9 8YN "O5'" P SING N N 10 8YN O2 C2 DOUB N N 11 8YN C1 C2 SING N N 12 8YN C1 C6 DOUB N N 13 8YN C2 N3 SING N N 14 8YN O1P P SING N N 15 8YN P O2P DOUB N N 16 8YN C6 N5 SING N N 17 8YN N3 C4 SING N N 18 8YN N5 C4 DOUB N N 19 8YN C4 N4 SING N N 20 8YN C6 H6 SING N N 21 8YN O1P H1 SING N N 22 8YN "C5'" "H52'" SING N N 23 8YN "C5'" "H51'" SING N N 24 8YN "C4'" "H4'" SING N N 25 8YN "C1'" "H1'" SING N N 26 8YN N3 H3 SING N N 27 8YN N4 H41 SING N N 28 8YN N4 H42 SING N N 29 8YN "C2'" "H22'" SING N N 30 8YN "C2'" "H21'" SING N N 31 8YN "C3'" "H3'" SING N N 32 8YN "O3'" H4 SING N N 33 8YN P O3P SING N N 34 8YN O3P H2 SING N N 35 # # 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 8YN InChI InChI 1.03 "InChI=1S/C9H14N3O7P/c10-9-11-2-4(8(14)12-9)6-1-5(13)7(19-6)3-18-20(15,16)17/h2,5-7,13H,1,3H2,(H2,15,16,17)(H3,10,11,12,14)/t5-,6+,7+/m0/s1" 8YN InChIKey InChI 1.03 LMPCXRMBUOVHQD-RRKCRQDMSA-N 8YN SMILES_CANONICAL CACTVS 3.385 "NC1=NC=C([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N1" 8YN SMILES CACTVS 3.385 "NC1=NC=C([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N1" 8YN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@H]1C2=CN=C(NC2=O)N)COP(=O)(O)O)O" 8YN SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1C2=CN=C(NC2=O)N)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id 8YN _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},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-pyrimidin-5-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 8YN "Create component" 2017-03-27 EBI 8YN "Initial release" 2017-06-28 RCSB 8YN "Other modification" 2019-05-07 EBI ##