data_DUZ # _chem_comp.id DUZ _chem_comp.name ;5-(benzylcarbamoyl)-2'-deoxyuridine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C17 H20 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-11-07 _chem_comp.pdbx_modified_date 2012-11-16 _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 441.329 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DUZ _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 4HQX _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 DUZ P P P 0 1 N N N 19.414 -16.869 18.595 6.299 1.850 0.186 P DUZ 1 DUZ N1 N1 N 0 1 N N N 18.981 -13.807 14.073 0.270 -1.080 0.141 N1 DUZ 2 DUZ C2 C2 C 0 1 N N N 19.001 -12.921 12.956 0.260 -0.655 -1.132 C2 DUZ 3 DUZ O2 O2 O 0 1 N N N 18.866 -13.364 11.797 1.300 -0.656 -1.761 O2 DUZ 4 DUZ N3 N3 N 0 1 N N N 19.168 -11.600 13.111 -0.863 -0.228 -1.734 N3 DUZ 5 DUZ C4 C4 C 0 1 N N N 19.300 -11.071 14.333 -2.035 -0.214 -1.064 C4 DUZ 6 DUZ O4 O4 O 0 1 N N N 19.444 -9.837 14.462 -3.056 0.170 -1.604 O4 DUZ 7 DUZ C5 C5 C 0 1 N N N 19.291 -11.977 15.514 -2.051 -0.675 0.333 C5 DUZ 8 DUZ C6 C6 C 0 1 N N N 19.097 -13.334 15.317 -0.862 -1.101 0.891 C6 DUZ 9 DUZ "C1'" "C1'" C 0 1 N N R 18.759 -15.241 13.877 1.530 -1.538 0.733 "C1'" DUZ 10 DUZ "C2'" "C2'" C 0 1 N N N 19.858 -16.176 14.354 2.020 -2.805 0.006 "C2'" DUZ 11 DUZ C21 C21 C 0 1 N N N 19.399 -11.496 16.924 -3.298 -0.683 1.113 C21 DUZ 12 DUZ O22 O22 O 0 1 N N N 19.442 -12.346 17.800 -3.314 -1.163 2.231 O22 DUZ 13 DUZ N23 N23 N 0 1 N N N 19.392 -10.190 17.196 -4.424 -0.158 0.589 N23 DUZ 14 DUZ C24 C24 C 0 1 N N N 19.420 -9.578 18.521 -5.637 -0.064 1.405 C24 DUZ 15 DUZ C25 C25 C 0 1 Y N N 17.974 -9.237 18.849 -6.744 0.554 0.590 C25 DUZ 16 DUZ C26 C26 C 0 1 Y N N 17.666 -8.381 19.901 -7.586 -0.250 -0.155 C26 DUZ 17 DUZ C27 C27 C 0 1 Y N N 16.335 -8.063 20.182 -8.601 0.317 -0.902 C27 DUZ 18 DUZ C28 C28 C 0 1 Y N N 15.287 -8.595 19.434 -8.774 1.688 -0.905 C28 DUZ 19 DUZ C29 C29 C 0 1 Y N N 15.589 -9.455 18.383 -7.932 2.492 -0.160 C29 DUZ 20 DUZ "C3'" "C3'" C 0 1 N N S 19.071 -17.401 14.776 3.420 -2.417 -0.531 "C3'" DUZ 21 DUZ "O3'" "O3'" O 0 1 N N N 18.750 -18.198 13.636 4.345 -3.494 -0.367 "O3'" DUZ 22 DUZ C30 C30 C 0 1 Y N N 16.920 -9.771 18.092 -6.921 1.925 0.592 C30 DUZ 23 DUZ "C4'" "C4'" C 0 1 N N R 17.724 -16.874 15.232 3.797 -1.221 0.380 "C4'" DUZ 24 DUZ "O4'" "O4'" O 0 1 N N N 17.589 -15.588 14.630 2.542 -0.531 0.566 "O4'" DUZ 25 DUZ "C5'" "C5'" C 0 1 N N N 17.582 -16.759 16.743 4.813 -0.314 -0.316 "C5'" DUZ 26 DUZ "O5'" "O5'" O 0 1 N N N 18.758 -16.175 17.299 5.231 0.713 0.585 "O5'" DUZ 27 DUZ OP1 OP1 O 0 1 N N N 19.264 -18.365 18.419 7.542 1.210 -0.299 OP1 DUZ 28 DUZ OP2 OP2 O 0 1 N N N 20.745 -16.239 18.902 5.685 2.779 -0.977 OP2 DUZ 29 DUZ OP3 OP3 O 0 1 N Y N 18.354 -16.473 19.719 6.628 2.754 1.477 OP3 DUZ 30 DUZ HN3 HN3 H 0 1 N N N 19.194 -11.005 12.307 -0.832 0.072 -2.656 HN3 DUZ 31 DUZ H6 H6 H 0 1 N N N 19.040 -14.004 16.162 -0.832 -1.447 1.914 H6 DUZ 32 DUZ "H1'" "H1'" H 0 1 N N N 18.579 -15.434 12.809 1.386 -1.750 1.792 "H1'" DUZ 33 DUZ "H2'" "H2'" H 0 1 N N N 20.561 -16.413 13.542 2.097 -3.639 0.704 "H2'" DUZ 34 DUZ "H2'A" "H2'A" H 0 0 N N N 20.410 -15.744 15.202 1.352 -3.056 -0.817 "H2'A" DUZ 35 DUZ HN23 HN23 H 0 0 N N N 19.365 -9.568 16.414 -4.431 0.157 -0.328 HN23 DUZ 36 DUZ H24 H24 H 0 1 N N N 19.825 -10.284 19.261 -5.936 -1.061 1.727 H24 DUZ 37 DUZ H24A H24A H 0 0 N N N 20.036 -8.666 18.509 -5.439 0.556 2.279 H24A DUZ 38 DUZ H26 H26 H 0 1 N N N 18.458 -7.961 20.503 -7.450 -1.322 -0.153 H26 DUZ 39 DUZ H27 H27 H 0 1 N N N 16.114 -7.390 20.997 -9.258 -0.312 -1.485 H27 DUZ 40 DUZ H28 H28 H 0 1 N N N 14.262 -8.345 19.665 -9.567 2.131 -1.489 H28 DUZ 41 DUZ H29 H29 H 0 1 N N N 14.793 -9.880 17.790 -8.068 3.564 -0.162 H29 DUZ 42 DUZ "H3'" "H3'" H 0 1 N N N 19.582 -17.963 15.571 3.364 -2.109 -1.575 "H3'" DUZ 43 DUZ "HO3'" "HO3'" H 0 0 N N N 18.257 -18.962 13.912 4.102 -4.298 -0.847 "HO3'" DUZ 44 DUZ H30 H30 H 0 1 N N N 17.140 -10.437 17.271 -6.266 2.553 1.178 H30 DUZ 45 DUZ "H4'" "H4'" H 0 1 N N N 16.938 -17.546 14.857 4.189 -1.573 1.334 "H4'" DUZ 46 DUZ "H5'" "H5'" H 0 1 N N N 16.714 -16.127 16.980 5.678 -0.903 -0.621 "H5'" DUZ 47 DUZ "H5'A" "H5'A" H 0 0 N N N 17.434 -17.761 17.173 4.354 0.139 -1.195 "H5'A" DUZ 48 DUZ HOP2 HOP2 H 0 0 N N N 21.410 -16.915 18.957 4.867 3.230 -0.729 HOP2 DUZ 49 DUZ HOP3 HOP3 H 0 0 N Y N 17.890 -17.251 20.006 7.267 3.461 1.309 HOP3 DUZ 50 # 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 DUZ "O5'" P SING N N 1 DUZ OP1 P DOUB N N 2 DUZ P OP2 SING N N 3 DUZ P OP3 SING N N 4 DUZ C2 N1 SING N N 5 DUZ "C1'" N1 SING N N 6 DUZ N1 C6 SING N N 7 DUZ O2 C2 DOUB N N 8 DUZ C2 N3 SING N N 9 DUZ N3 C4 SING N N 10 DUZ N3 HN3 SING N N 11 DUZ C4 O4 DOUB N N 12 DUZ C4 C5 SING N N 13 DUZ C6 C5 DOUB N N 14 DUZ C5 C21 SING N N 15 DUZ C6 H6 SING N N 16 DUZ "C1'" "C2'" SING N N 17 DUZ "C1'" "O4'" SING N N 18 DUZ "C1'" "H1'" SING N N 19 DUZ "C2'" "C3'" SING N N 20 DUZ "C2'" "H2'" SING N N 21 DUZ "C2'" "H2'A" SING N N 22 DUZ C21 N23 SING N N 23 DUZ C21 O22 DOUB N N 24 DUZ N23 C24 SING N N 25 DUZ N23 HN23 SING N N 26 DUZ C24 C25 SING N N 27 DUZ C24 H24 SING N N 28 DUZ C24 H24A SING N N 29 DUZ C30 C25 DOUB Y N 30 DUZ C25 C26 SING Y N 31 DUZ C26 C27 DOUB Y N 32 DUZ C26 H26 SING N N 33 DUZ C28 C27 SING Y N 34 DUZ C27 H27 SING N N 35 DUZ C29 C28 DOUB Y N 36 DUZ C28 H28 SING N N 37 DUZ C30 C29 SING Y N 38 DUZ C29 H29 SING N N 39 DUZ "O3'" "C3'" SING N N 40 DUZ "C3'" "C4'" SING N N 41 DUZ "C3'" "H3'" SING N N 42 DUZ "O3'" "HO3'" SING N N 43 DUZ C30 H30 SING N N 44 DUZ "O4'" "C4'" SING N N 45 DUZ "C4'" "C5'" SING N N 46 DUZ "C4'" "H4'" SING N N 47 DUZ "C5'" "O5'" SING N N 48 DUZ "C5'" "H5'" SING N N 49 DUZ "C5'" "H5'A" SING N N 50 DUZ OP2 HOP2 SING N N 51 DUZ OP3 HOP3 SING N N 52 # 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 DUZ SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(N2C(=O)NC(=O)C(C(=O)NCc1ccccc1)=C2)CC3O" DUZ InChI InChI 1.03 "InChI=1S/C17H20N3O9P/c21-12-6-14(29-13(12)9-28-30(25,26)27)20-8-11(16(23)19-17(20)24)15(22)18-7-10-4-2-1-3-5-10/h1-5,8,12-14,21H,6-7,9H2,(H,18,22)(H,19,23,24)(H2,25,26,27)/t12-,13+,14+/m0/s1" DUZ InChIKey InChI 1.03 RDNHEZYEIYMTCG-BFHYXJOUSA-N DUZ SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3ccccc3)C(=O)NC2=O" DUZ SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3ccccc3)C(=O)NC2=O" DUZ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CNC(=O)C2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" DUZ SMILES "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CNC(=O)C2=CN(C(=O)NC2=O)C3CC(C(O3)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 DUZ "SYSTEMATIC NAME" ACDLabs 12.01 ;5-(benzylcarbamoyl)-2'-deoxyuridine 5'-(dihydrogen phosphate) ; DUZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-5-[(phenylmethyl)carbamoyl]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 DUZ "Create component" 2012-11-07 RCSB DUZ "Initial release" 2012-11-16 RCSB #