data_18Q # _chem_comp.id 18Q _chem_comp.name ;2'-deoxy-5-[(thiophen-2-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C15 H18 N3 O9 P S" _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 447.357 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 18Q _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 18Q P P P 0 1 N N N 2.409 -6.046 6.582 6.334 1.898 0.168 P 18Q 1 18Q N1 N1 N 0 1 N N N 1.875 -11.423 7.476 0.352 -1.126 0.145 N1 18Q 2 18Q C2 C2 C 0 1 N N N 1.490 -12.734 7.871 0.349 -0.738 -1.140 C2 18Q 3 18Q O2 O2 O 0 1 N N N 1.172 -13.592 7.012 1.395 -0.742 -1.758 O2 18Q 4 18Q N3 N3 N 0 1 N N N 1.466 -13.077 9.168 -0.775 -0.347 -1.765 N3 18Q 5 18Q C4 C4 C 0 1 N N N 1.801 -12.199 10.122 -1.954 -0.332 -1.108 C4 18Q 6 18Q O4 O4 O 0 1 N N N 1.773 -12.545 11.321 -2.974 0.021 -1.669 O4 18Q 7 18Q C5 C5 C 0 1 N N N 2.205 -10.819 9.734 -1.977 -0.752 0.302 C5 18Q 8 18Q C6 C6 C 0 1 N N N 2.229 -10.500 8.385 -0.787 -1.143 0.885 C6 18Q 9 18Q "C1'" "C1'" C 0 1 N N R 1.904 -11.075 6.052 1.612 -1.546 0.763 "C1'" 18Q 10 18Q "C2'" "C2'" C 0 1 N N N 0.803 -10.083 5.678 2.130 -2.826 0.078 "C2'" 18Q 11 18Q C21 C21 C 0 1 N N N 2.610 -9.791 10.751 -3.232 -0.755 1.069 C21 18Q 12 18Q O22 O22 O 0 1 N N N 2.856 -8.655 10.390 -3.252 -1.202 2.201 O22 18Q 13 18Q N23 N23 N 0 1 N N N 2.719 -10.132 12.029 -4.360 -0.264 0.519 N23 18Q 14 18Q C24 C24 C 0 1 N N N 3.128 -9.218 13.082 -5.582 -0.164 1.320 C24 18Q 15 18Q C25 C25 C 0 1 Y N N 4.632 -9.295 13.113 -6.690 0.413 0.476 C25 18Q 16 18Q S26 S26 S 0 1 Y N N 5.518 -7.818 12.948 -7.053 2.126 0.314 S26 18Q 17 18Q C27 C27 C 0 1 Y N N 7.079 -8.546 13.053 -8.384 1.771 -0.780 C27 18Q 18 18Q C28 C28 C 0 1 Y N N 6.842 -9.910 13.213 -8.479 0.452 -0.955 C28 18Q 19 18Q C29 C29 C 0 1 Y N N 5.513 -10.336 13.248 -7.541 -0.297 -0.266 C29 18Q 20 18Q "C3'" "C3'" C 0 1 N N S 1.423 -9.389 4.488 3.529 -2.432 -0.455 "C3'" 18Q 21 18Q "O3'" "O3'" O 0 1 N N N 1.194 -10.284 3.397 4.469 -3.489 -0.251 "O3'" 18Q 22 18Q "C4'" "C4'" C 0 1 N N R 2.922 -9.409 4.750 3.878 -1.205 0.424 "C4'" 18Q 23 18Q "O4'" "O4'" O 0 1 N N N 3.155 -10.476 5.684 2.610 -0.527 0.580 "O4'" 18Q 24 18Q "C5'" "C5'" C 0 1 N N N 3.468 -8.078 5.262 4.887 -0.302 -0.287 "C5'" 18Q 25 18Q "O5'" "O5'" O 0 1 N N N 2.664 -7.622 6.344 5.279 0.757 0.589 "O5'" 18Q 26 18Q OP1 OP1 O 0 1 N N N 1.299 -5.848 7.585 6.636 2.844 1.435 OP1 18Q 27 18Q OP2 OP2 O 0 1 N N N 2.292 -5.372 5.234 7.592 1.264 -0.286 OP2 18Q 28 18Q OP3 OP3 O 0 1 N Y N 3.805 -5.607 7.234 5.718 2.784 -1.028 OP3 18Q 29 18Q HN3 HN3 H 0 1 N N N 1.193 -14.004 9.427 -0.738 -0.074 -2.695 HN3 18Q 30 18Q H6 H6 H 0 1 N N N 2.531 -9.513 8.066 -0.763 -1.458 1.917 H6 18Q 31 18Q "H1'" "H1'" H 0 1 N N N 1.753 -11.990 5.460 1.461 -1.730 1.826 "H1'" 18Q 32 18Q "H2'" "H2'" H 0 1 N N N -0.128 -10.600 5.403 2.212 -3.639 0.800 "H2'" 18Q 33 18Q "H2'A" "H2'A" H 0 0 N N N 0.602 -9.376 6.497 1.473 -3.112 -0.743 "H2'A" 18Q 34 18Q HN23 HN23 H 0 0 N N N 2.507 -11.076 12.283 -4.362 0.024 -0.407 HN23 18Q 35 18Q H24 H24 H 0 1 N N N 2.799 -8.194 12.852 -5.870 -1.156 1.668 H24 18Q 36 18Q H24A H24A H 0 0 N N N 2.706 -9.530 14.049 -5.403 0.485 2.177 H24A 18Q 37 18Q H27 H27 H 0 1 N N N 8.037 -8.050 13.005 -9.026 2.508 -1.239 H27 18Q 38 18Q H28 H28 H 0 1 N N N 7.657 -10.612 13.307 -9.228 0.002 -1.590 H28 18Q 39 18Q H29 H29 H 0 1 N N N 5.214 -11.367 13.368 -7.503 -1.375 -0.322 H29 18Q 40 18Q "H3'" "H3'" H 0 1 N N N 1.031 -8.373 4.331 3.480 -2.155 -1.508 "H3'" 18Q 41 18Q "HO3'" "HO3'" H 0 0 N N N 1.559 -9.914 2.602 4.244 -4.310 -0.711 "HO3'" 18Q 42 18Q "H4'" "H4'" H 0 1 N N N 3.430 -9.642 3.803 4.265 -1.523 1.392 "H4'" 18Q 43 18Q "H5'" "H5'" H 0 1 N N N 4.504 -8.214 5.606 5.764 -0.886 -0.566 "H5'" 18Q 44 18Q "H5'A" "H5'A" H 0 0 N N N 3.446 -7.336 4.450 4.431 0.118 -1.183 "H5'A" 18Q 45 18Q HOP1 HOP1 H 0 0 N N N 0.629 -5.288 7.210 7.265 3.556 1.254 HOP1 18Q 46 18Q HOP3 HOP3 H 0 0 N Y N 4.261 -5.021 6.642 4.891 3.230 -0.801 HOP3 18Q 47 # 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 18Q OP2 P DOUB N N 1 18Q "O5'" P SING N N 2 18Q P OP3 SING N N 3 18Q P OP1 SING N N 4 18Q "C1'" N1 SING N N 5 18Q N1 C2 SING N N 6 18Q N1 C6 SING N N 7 18Q O2 C2 DOUB N N 8 18Q C2 N3 SING N N 9 18Q N3 C4 SING N N 10 18Q N3 HN3 SING N N 11 18Q C5 C4 SING N N 12 18Q C4 O4 DOUB N N 13 18Q C6 C5 DOUB N N 14 18Q C5 C21 SING N N 15 18Q C6 H6 SING N N 16 18Q "C2'" "C1'" SING N N 17 18Q "O4'" "C1'" SING N N 18 18Q "C1'" "H1'" SING N N 19 18Q "C3'" "C2'" SING N N 20 18Q "C2'" "H2'" SING N N 21 18Q "C2'" "H2'A" SING N N 22 18Q O22 C21 DOUB N N 23 18Q C21 N23 SING N N 24 18Q N23 C24 SING N N 25 18Q N23 HN23 SING N N 26 18Q C24 C25 SING N N 27 18Q C24 H24 SING N N 28 18Q C24 H24A SING N N 29 18Q S26 C25 SING Y N 30 18Q C25 C29 DOUB Y N 31 18Q S26 C27 SING Y N 32 18Q C27 C28 DOUB Y N 33 18Q C27 H27 SING N N 34 18Q C28 C29 SING Y N 35 18Q C28 H28 SING N N 36 18Q C29 H29 SING N N 37 18Q "O3'" "C3'" SING N N 38 18Q "C3'" "C4'" SING N N 39 18Q "C3'" "H3'" SING N N 40 18Q "O3'" "HO3'" SING N N 41 18Q "C4'" "C5'" SING N N 42 18Q "C4'" "O4'" SING N N 43 18Q "C4'" "H4'" SING N N 44 18Q "C5'" "O5'" SING N N 45 18Q "C5'" "H5'" SING N N 46 18Q "C5'" "H5'A" SING N N 47 18Q OP1 HOP1 SING N N 48 18Q OP3 HOP3 SING N N 49 # 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 18Q SMILES ACDLabs 12.01 "O=C(NCc1sccc1)C2=CN(C(=O)NC2=O)C3OC(COP(=O)(O)O)C(O)C3" 18Q InChI InChI 1.03 "InChI=1S/C15H18N3O9PS/c19-10-4-12(27-11(10)7-26-28(23,24)25)18-6-9(14(21)17-15(18)22)13(20)16-5-8-2-1-3-29-8/h1-3,6,10-12,19H,4-5,7H2,(H,16,20)(H,17,21,22)(H2,23,24,25)/t10-,11+,12+/m0/s1" 18Q InChIKey InChI 1.03 OUBFLYZWEMDJOL-QJPTWQEYSA-N 18Q SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3sccc3)C(=O)NC2=O" 18Q SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCc3sccc3)C(=O)NC2=O" 18Q SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc(sc1)CNC(=O)C2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" 18Q SMILES "OpenEye OEToolkits" 1.7.6 "c1cc(sc1)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 18Q "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-5-[(thiophen-2-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate) ; 18Q "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-5-(thiophen-2-ylmethylcarbamoyl)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 18Q "Create component" 2012-11-07 RCSB 18Q "Initial release" 2012-11-16 RCSB #