data_Z # _chem_comp.id Z _chem_comp.name "1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)PYRIMIDIN-2(1H)-ONE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "2'-DEOXYZEBULARINE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-09-09 _chem_comp.pdbx_modified_date 2021-03-01 _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 292.182 _chem_comp.one_letter_code C _chem_comp.three_letter_code Z _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1M0E _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 Z P P P 0 1 N N N -18.687 43.594 84.855 -3.968 -1.665 3.118 P Z 1 Z OP1 O1P O 0 1 N N N -17.220 43.475 85.067 -4.406 -2.599 4.208 OP1 Z 2 Z OP2 O2P O 0 1 N N N -19.212 44.047 83.533 -3.912 -2.311 1.636 OP2 Z 3 Z "O5'" O5* O 0 1 N N N -19.307 42.178 85.220 -2.493 -1.028 3.315 "O5'" Z 4 Z "C5'" C5* C 0 1 N N N -18.592 41.289 86.108 -2.005 -0.136 2.327 "C5'" Z 5 Z "C4'" C4* C 0 1 N N R -19.123 39.881 85.986 -0.611 0.328 2.728 "C4'" Z 6 Z "O4'" O4* O 0 1 N N N -18.724 39.267 84.747 0.247 -0.829 2.764 "O4'" Z 7 Z "C3'" C3* C 0 1 N N S -18.581 38.952 87.059 0.008 1.286 1.720 "C3'" Z 8 Z "O3'" O3* O 0 1 N N N -19.449 39.080 88.181 0.965 2.121 2.368 "O3'" Z 9 Z "C2'" C2* C 0 1 N N N -18.727 37.580 86.427 0.710 0.360 0.754 "C2'" Z 10 Z "C1'" C1* C 0 1 N N R -18.724 37.856 84.924 1.157 -0.778 1.657 "C1'" Z 11 Z N1 N1 N 0 1 N N N -17.632 37.273 84.118 1.164 -2.047 0.989 N1 Z 12 Z C2 C2 C 0 1 N N N -17.651 37.469 82.744 2.354 -2.526 0.378 C2 Z 13 Z O2 O2 O 0 1 N N N -18.555 38.171 82.253 3.395 -1.868 0.410 O2 Z 14 Z N3 N3 N 0 1 N N N -16.691 36.899 81.982 2.324 -3.757 -0.260 N3 Z 15 Z C4 C4 C 0 1 N N N -15.726 36.172 82.550 1.219 -4.426 -0.276 C4 Z 16 Z C5 C5 C 0 1 N N N -15.618 36.054 83.962 -0.047 -3.999 0.331 C5 Z 17 Z C6 C6 C 0 1 N N N -16.430 36.867 84.705 0.006 -2.813 0.937 C6 Z 18 Z OP3 O3P O 0 1 N Y N ? ? ? -4.901 -0.360 2.920 OP3 Z 19 Z HOP2 2HOP H 0 0 N N N -20.149 44.123 83.397 -4.684 -2.823 1.313 HOP2 Z 20 Z "H5'" 1H5* H 0 1 N N N -17.490 41.332 85.940 -1.971 -0.654 1.366 "H5'" Z 21 Z "H5''" 2H5* H 0 0 N N N -18.613 41.650 87.162 -2.683 0.718 2.254 "H5''" Z 22 Z "H4'" H4* H 0 1 N N N -20.228 39.999 86.068 -0.644 0.753 3.736 "H4'" Z 23 Z "H3'" H3* H 0 1 N N N -17.534 39.151 87.388 -0.722 1.941 1.236 "H3'" Z 24 Z "HO3'" H3T H 0 0 N Y N -19.110 38.499 88.852 0.738 3.042 2.152 "HO3'" Z 25 Z "H2'" 1H2* H 0 1 N N N -17.960 36.841 86.757 -0.003 -0.001 0.003 "H2'" Z 26 Z "H2''" 2H2* H 0 0 N N N -19.612 37.004 86.784 1.556 0.818 0.232 "H2''" Z 27 Z "H1'" H1* H 0 1 N N N -19.634 37.341 84.537 2.163 -0.604 2.054 "H1'" Z 28 Z H4 H4 H 0 1 N N N -15.024 35.673 81.859 1.193 -5.404 -0.783 H4 Z 29 Z H5 H5 H 0 1 N N N -14.927 35.355 84.464 -0.931 -4.617 0.274 H5 Z 30 Z H6 H6 H 0 1 N N N -16.132 37.177 85.720 -0.867 -2.391 1.422 H6 Z 31 Z HOP3 3HOP H 0 0 N N N -0.937 0.076 -0.135 -5.874 -0.475 2.871 HOP3 Z 32 # # 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 Z P OP1 DOUB N N 1 Z P OP2 SING N N 2 Z P "O5'" SING N N 3 Z P OP3 SING N N 4 Z OP2 HOP2 SING N N 5 Z "O5'" "C5'" SING N N 6 Z "C5'" "C4'" SING N N 7 Z "C5'" "H5'" SING N N 8 Z "C5'" "H5''" SING N N 9 Z "C4'" "O4'" SING N N 10 Z "C4'" "C3'" SING N N 11 Z "C4'" "H4'" SING N N 12 Z "O4'" "C1'" SING N N 13 Z "C3'" "O3'" SING N N 14 Z "C3'" "C2'" SING N N 15 Z "C3'" "H3'" SING N N 16 Z "O3'" "HO3'" SING N N 17 Z "C2'" "C1'" SING N N 18 Z "C2'" "H2'" SING N N 19 Z "C2'" "H2''" SING N N 20 Z "C1'" N1 SING N N 21 Z "C1'" "H1'" SING N N 22 Z N1 C2 SING N N 23 Z N1 C6 SING N N 24 Z C2 O2 DOUB N N 25 Z C2 N3 SING N N 26 Z N3 C4 DOUB N N 27 Z C4 C5 SING N N 28 Z C4 H4 SING N N 29 Z C5 C6 DOUB N N 30 Z C5 H5 SING N N 31 Z C6 H6 SING N N 32 Z OP3 HOP3 SING N N 33 # # 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 Z SMILES ACDLabs 10.04 "O=C1N=CC=CN1C2OC(C(O)C2)COP(=O)(O)O" Z SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC=NC2=O" Z SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC=NC2=O" Z SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC=NC2=O)COP(=O)(O)O)O" Z SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC=NC2=O)COP(=O)(O)O)O" Z InChI InChI 1.03 "InChI=1S/C9H13N2O7P/c12-6-4-8(11-3-1-2-10-9(11)13)18-7(6)5-17-19(14,15)16/h1-3,6-8,12H,4-5H2,(H2,14,15,16)/t6-,7+,8+/m0/s1" Z InChIKey InChI 1.03 KOQACCDGALTLCX-XLPZGREQSA-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 Z "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)pyrimidin-2(1H)-one" Z "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(2-oxopyrimidin-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 Z "Create component" 2002-09-09 EBI Z "Modify descriptor" 2011-06-04 RCSB Z "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id Z _pdbx_chem_comp_synonyms.name "2'-DEOXYZEBULARINE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##