data_XCT # _chem_comp.id XCT _chem_comp.name "4-AMINO-1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)PYRIMIDIN-2(1H)-ONE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL CYTOSINE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-06-20 _chem_comp.pdbx_modified_date 2021-03-13 _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 321.224 _chem_comp.one_letter_code C _chem_comp.three_letter_code XCT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2H9S _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 XCT OP3 O3P O 0 1 N Y N 3.151 7.855 17.218 -3.576 1.731 1.510 OP3 XCT 1 XCT P P P 0 1 N N N 4.516 7.310 17.808 -3.751 1.344 -0.043 P XCT 2 XCT OP1 O1P O 0 1 N N N 4.700 5.943 17.290 -4.870 0.387 -0.190 OP1 XCT 3 XCT OP2 O2P O 0 1 N N N 4.498 7.567 19.267 -4.067 2.674 -0.895 OP2 XCT 4 XCT "O6'" "O6'" O 0 1 N N N 5.650 8.219 17.165 -2.393 0.670 -0.585 "O6'" XCT 5 XCT "C6'" "C6'" C 0 1 N N N 6.924 8.281 17.689 -2.231 -0.560 0.125 "C6'" XCT 6 XCT "C5'" "C5'" C 0 1 N N R 7.570 9.579 17.266 -0.951 -1.255 -0.345 "C5'" XCT 7 XCT "O5'" "O5'" O 0 1 N N N 6.855 10.659 17.892 0.178 -0.457 0.008 "O5'" XCT 8 XCT "C4'" "C4'" C 0 1 N N S 9.023 9.679 17.685 -0.843 -2.627 0.324 "C4'" XCT 9 XCT "O4'" "O4'" O 0 1 N N N 9.708 8.606 17.067 -1.989 -3.414 -0.008 "O4'" XCT 10 XCT "C3'" "C3'" C 0 1 N N N 9.490 11.036 17.221 0.424 -3.329 -0.178 "C3'" XCT 11 XCT "C2'" "C2'" C 0 1 N N N 8.683 12.173 17.860 1.621 -2.397 0.046 "C2'" XCT 12 XCT "C1'" "C1'" C 0 1 N N R 7.232 11.943 17.431 1.327 -1.042 -0.602 "C1'" XCT 13 XCT N1 N1 N 0 1 N N N 6.291 12.879 18.051 2.479 -0.156 -0.421 N1 XCT 14 XCT C2 C2 C 0 1 N N N 5.433 13.644 17.270 2.831 0.241 0.815 C2 XCT 15 XCT O2 O2 O 0 1 N N N 5.545 13.597 16.012 2.185 -0.144 1.776 O2 XCT 16 XCT C6 C6 C 0 1 N N N 6.218 12.913 19.414 3.188 0.263 -1.507 C6 XCT 17 XCT C5 C5 C 0 1 N N N 5.367 13.719 20.026 4.247 1.088 -1.328 C5 XCT 18 XCT C4 C4 C 0 1 N N N 4.497 14.504 19.243 4.594 1.480 -0.018 C4 XCT 19 XCT N3 N3 N 0 1 N N N 4.560 14.484 17.890 3.874 1.046 1.008 N3 XCT 20 XCT N4 N4 N 0 1 N N N 3.624 15.316 19.841 5.668 2.312 0.193 N4 XCT 21 XCT HOP3 3HOP H 0 0 N N N 2.522 7.964 17.922 -2.838 2.355 1.561 HOP3 XCT 22 XCT HOP2 2HOP H 0 0 N N N 4.494 6.740 19.735 -4.885 3.046 -0.539 HOP2 XCT 23 XCT "H6'1" "1H6'" H 0 0 N N N 7.519 7.433 17.318 -3.087 -1.206 -0.067 "H6'1" XCT 24 XCT "H6'2" "2H6'" H 0 0 N N N 6.874 8.235 18.787 -2.162 -0.356 1.194 "H6'2" XCT 25 XCT "H5'" "H5'" H 0 1 N N N 7.532 9.626 16.168 -0.984 -1.381 -1.427 "H5'" XCT 26 XCT "H4'" "H4'" H 0 1 N N N 9.198 9.599 18.768 -0.787 -2.503 1.405 "H4'" XCT 27 XCT H4T H4T H 0 1 N N N 9.862 8.812 16.153 -1.875 -4.270 0.428 H4T XCT 28 XCT "H3'1" "1H3'" H 0 0 N N N 9.350 11.090 16.131 0.325 -3.548 -1.241 "H3'1" XCT 29 XCT "H3'2" "2H3'" H 0 0 N N N 10.548 11.157 17.498 0.573 -4.255 0.377 "H3'2" XCT 30 XCT "H2'1" "1H2'" H 0 0 N N N 9.048 13.159 17.537 2.512 -2.833 -0.408 "H2'1" XCT 31 XCT "H2'2" "2H2'" H 0 0 N N N 8.774 12.147 18.956 1.784 -2.263 1.115 "H2'2" XCT 32 XCT "H1'" "H1'" H 0 1 N N N 7.190 12.068 16.339 1.140 -1.183 -1.666 "H1'" XCT 33 XCT H6 H6 H 0 1 N N N 6.863 12.274 19.999 2.905 -0.055 -2.499 H6 XCT 34 XCT H5 H5 H 0 1 N N N 5.339 13.775 21.104 4.823 1.432 -2.174 H5 XCT 35 XCT HN41 1HN4 H 0 0 N N N 2.981 15.920 19.370 5.902 2.584 1.094 HN41 XCT 36 XCT HN42 2HN4 H 0 0 N N N 3.712 15.228 20.833 6.195 2.625 -0.560 HN42 XCT 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 XCT OP3 P SING N N 1 XCT OP3 HOP3 SING N N 2 XCT P OP1 DOUB N N 3 XCT P OP2 SING N N 4 XCT P "O6'" SING N N 5 XCT OP2 HOP2 SING N N 6 XCT "O6'" "C6'" SING N N 7 XCT "C6'" "C5'" SING N N 8 XCT "C6'" "H6'1" SING N N 9 XCT "C6'" "H6'2" SING N N 10 XCT "C5'" "O5'" SING N N 11 XCT "C5'" "C4'" SING N N 12 XCT "C5'" "H5'" SING N N 13 XCT "O5'" "C1'" SING N N 14 XCT "C4'" "O4'" SING N N 15 XCT "C4'" "C3'" SING N N 16 XCT "C4'" "H4'" SING N N 17 XCT "O4'" H4T SING N N 18 XCT "C3'" "C2'" SING N N 19 XCT "C3'" "H3'1" SING N N 20 XCT "C3'" "H3'2" SING N N 21 XCT "C2'" "C1'" SING N N 22 XCT "C2'" "H2'1" SING N N 23 XCT "C2'" "H2'2" SING N N 24 XCT "C1'" N1 SING N N 25 XCT "C1'" "H1'" SING N N 26 XCT N1 C2 SING N N 27 XCT N1 C6 SING N N 28 XCT C2 O2 DOUB N N 29 XCT C2 N3 SING N N 30 XCT C6 C5 DOUB N N 31 XCT C6 H6 SING N N 32 XCT C5 C4 SING N N 33 XCT C5 H5 SING N N 34 XCT C4 N3 DOUB N N 35 XCT C4 N4 SING N N 36 XCT N4 HN41 SING N N 37 XCT N4 HN42 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 XCT SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)CC2)COP(=O)(O)O" XCT SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@H]2CC[C@H](O)[C@@H](CO[P](O)(O)=O)O2" XCT SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2CC[CH](O)[CH](CO[P](O)(O)=O)O2" XCT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@@H](O[C@@H]([C@H]1O)COP(=O)(O)O)N2C=CC(=NC2=O)N" XCT SMILES "OpenEye OEToolkits" 1.5.0 "C1CC(OC(C1O)COP(=O)(O)O)N2C=CC(=NC2=O)N" XCT InChI InChI 1.03 "InChI=1S/C10H16N3O7P/c11-8-3-4-13(10(15)12-8)9-2-1-6(14)7(20-9)5-19-21(16,17)18/h3-4,6-7,9,14H,1-2,5H2,(H2,11,12,15)(H2,16,17,18)/t6-,7+,9+/m0/s1" XCT InChIKey InChI 1.03 ZOFWVGAMLXMFAU-LKEWCRSYSA-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 XCT "SYSTEMATIC NAME" ACDLabs 10.04 "4-amino-1-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)pyrimidin-2(1H)-one" XCT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,6R)-6-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxan-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 XCT "Create component" 2006-06-20 RCSB XCT "Modify descriptor" 2011-06-04 RCSB XCT "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XCT _pdbx_chem_comp_synonyms.name "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL CYTOSINE" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##