data_3KA # _chem_comp.id 3KA _chem_comp.name "1-(2-deoxy-5-O-phosphono-beta-L-erythro-pentofuranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "L-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-09-03 _chem_comp.pdbx_modified_date 2020-06-17 _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 308.182 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3KA _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 4WB2 _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 3KA O4 O1 O 0 1 N N N -11.640 20.119 30.744 -5.255 -2.615 -0.375 O4 3KA 1 3KA C4 C1 C 0 1 N N N -11.260 18.934 30.884 -4.371 -1.803 -0.172 C4 3KA 2 3KA N3 N1 N 0 1 N N N -9.965 18.681 31.103 -4.663 -0.491 -0.068 N3 3KA 3 3KA C2 C2 C 0 1 N N N -9.528 17.429 31.270 -3.684 0.406 0.155 C2 3KA 4 3KA O2 O2 O 0 1 N N N -8.312 17.202 31.468 -3.963 1.586 0.247 O2 3KA 5 3KA C5 C3 C 0 1 N N N -12.184 17.894 30.826 -3.027 -2.228 -0.038 C5 3KA 6 3KA C6 C4 C 0 1 N N N -11.740 16.589 30.996 -2.066 -1.307 0.187 C6 3KA 7 3KA N1 N2 N 0 1 N N N -10.437 16.358 31.200 -2.403 0.016 0.280 N1 3KA 8 3KA "C1'" C5 C 0 1 N N S -9.956 14.999 31.438 -1.360 1.015 0.523 "C1'" 3KA 9 3KA "O4'" O3 O 0 1 N N N -10.851 14.465 32.426 -0.062 0.388 0.596 "O4'" 3KA 10 3KA "C2'" C6 C 0 1 N N N -10.013 14.007 30.287 -1.231 1.975 -0.688 "C2'" 3KA 11 3KA "C3'" C7 C 0 1 N N R -10.141 12.714 31.068 0.227 2.477 -0.549 "C3'" 3KA 12 3KA "O3'" O4 O 0 1 N N N -8.892 12.437 31.707 0.258 3.749 0.101 "O3'" 3KA 13 3KA "C4'" C8 C 0 1 N N S -11.091 13.073 32.193 0.913 1.408 0.324 "C4'" 3KA 14 3KA "C5'" C9 C 0 1 N N N -12.554 12.837 31.817 2.101 0.806 -0.429 "C5'" 3KA 15 3KA "O5'" O5 O 0 1 N N N -13.295 12.850 33.026 2.800 -0.098 0.429 "O5'" 3KA 16 3KA P P1 P 0 1 N N N -14.862 12.518 33.110 4.108 -0.915 -0.036 P 3KA 17 3KA OP1 O6 O 0 1 N N N -15.257 11.478 32.087 3.799 -1.682 -1.263 OP1 3KA 18 3KA OP2 O7 O 0 1 N N N -15.169 12.266 34.568 5.307 0.117 -0.335 OP2 3KA 19 3KA O1 O8 O 0 1 N Y N -15.553 13.915 32.695 4.551 -1.929 1.133 O1 3KA 20 3KA H1 H1 H 0 1 N N N -9.314 19.439 31.142 -5.581 -0.192 -0.156 H1 3KA 21 3KA H2 H2 H 0 1 N N N -13.230 18.099 30.651 -2.775 -3.276 -0.113 H2 3KA 22 3KA H3 H3 H 0 1 N N N -12.440 15.767 30.964 -1.035 -1.613 0.292 H3 3KA 23 3KA H4 H4 H 0 1 N N N -8.930 15.031 31.833 -1.569 1.572 1.436 H4 3KA 24 3KA H5 H5 H 0 1 N N N -9.095 14.030 29.681 -1.370 1.438 -1.626 H5 3KA 25 3KA H6 H6 H 0 1 N N N -10.885 14.182 29.639 -1.936 2.801 -0.606 H6 3KA 26 3KA H7 H7 H 0 1 N N N -10.517 11.886 30.449 0.704 2.538 -1.527 H7 3KA 27 3KA H8 H8 H 0 1 N N N -8.961 11.628 32.200 -0.211 4.447 -0.377 H8 3KA 28 3KA H9 H9 H 0 1 N N N -10.844 12.480 33.086 1.253 1.855 1.259 H9 3KA 29 3KA H10 H10 H 0 1 N N N -12.907 13.636 31.148 1.740 0.269 -1.306 H10 3KA 30 3KA H11 H11 H 0 1 N N N -12.664 11.864 31.316 2.775 1.603 -0.743 H11 3KA 31 3KA H12 H12 H 0 1 N N N -15.602 11.425 34.660 5.562 0.655 0.427 H12 3KA 32 3KA H13 H13 H 0 1 N N N -16.060 13.794 31.901 5.334 -2.455 0.922 H13 3KA 33 # # 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 3KA "C2'" "C3'" SING N N 1 3KA "C2'" "C1'" SING N N 2 3KA O4 C4 DOUB N N 3 3KA C5 C4 SING N N 4 3KA C5 C6 DOUB N N 5 3KA C4 N3 SING N N 6 3KA C6 N1 SING N N 7 3KA "C3'" "O3'" SING N N 8 3KA "C3'" "C4'" SING N N 9 3KA N3 C2 SING N N 10 3KA N1 C2 SING N N 11 3KA N1 "C1'" SING N N 12 3KA C2 O2 DOUB N N 13 3KA "C1'" "O4'" SING N N 14 3KA "C5'" "C4'" SING N N 15 3KA "C5'" "O5'" SING N N 16 3KA OP1 P DOUB N N 17 3KA "C4'" "O4'" SING N N 18 3KA "O5'" P SING N N 19 3KA P OP2 SING N N 20 3KA P O1 SING N N 21 3KA N3 H1 SING N N 22 3KA C5 H2 SING N N 23 3KA C6 H3 SING N N 24 3KA "C1'" H4 SING N N 25 3KA "C2'" H5 SING N N 26 3KA "C2'" H6 SING N N 27 3KA "C3'" H7 SING N N 28 3KA "O3'" H8 SING N N 29 3KA "C4'" H9 SING N N 30 3KA "C5'" H10 SING N N 31 3KA "C5'" H11 SING N N 32 3KA OP2 H12 SING N N 33 3KA O1 H13 SING N N 34 # # 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 3KA SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O" 3KA InChI InChI 1.03 "InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m1/s1" 3KA InChIKey InChI 1.03 JSRLJPSBLDHEIO-CHKWXVPMSA-N 3KA SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1C[C@H](O[C@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" 3KA SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" 3KA SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C1[C@H]([C@@H](O[C@@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" 3KA SMILES "OpenEye OEToolkits" 1.9.2 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=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 3KA "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-5-O-phosphono-beta-L-erythro-pentofuranosyl)pyrimidine-2,4(1H,3H)-dione" 3KA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2S,3R,5S)-5-[2,4-bis(oxidanylidene)pyrimidin-1-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 3KA "Create component" 2014-09-03 EBI 3KA "Modify descriptor" 2014-09-05 RCSB 3KA "Initial release" 2015-05-06 RCSB 3KA "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3KA _pdbx_chem_comp_synonyms.name "L-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##