data_08Q # _chem_comp.id 08Q _chem_comp.name "5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H20 N3 O7 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-10-15 _chem_comp.pdbx_modified_date 2012-04-20 _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 381.342 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 08Q _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 3U6D _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 08Q P P P 0 1 N N N 4.255 -8.547 16.061 3.176 1.672 -0.914 P 08Q 1 08Q OP1 OP1 O 0 1 N N N 3.332 -8.497 17.195 2.956 2.043 -2.330 OP1 08Q 2 08Q "C8'" "C8'" C 0 1 N N N 4.196 -5.161 14.105 5.221 -1.111 0.666 "C8'" 08Q 3 08Q "C7'" "C7'" C 0 1 N N N 4.782 -6.345 14.823 4.832 0.367 0.609 "C7'" 08Q 4 08Q "C5'" "C5'" C 0 1 N N N 4.457 -11.249 15.793 1.402 -0.319 -1.088 "C5'" 08Q 5 08Q "O5'" "O5'" O 0 1 N N N 4.160 -9.919 15.224 1.923 0.811 -0.384 "O5'" 08Q 6 08Q "C4'" "C4'" C 0 1 N N R 3.448 -11.983 16.802 0.219 -0.902 -0.312 "C4'" 08Q 7 08Q "O4'" "O4'" O 0 1 N N N 3.239 -11.271 18.185 -0.867 0.033 -0.307 "O4'" 08Q 8 08Q "C3'" "C3'" C 0 1 N N S 2.093 -12.502 16.736 -0.277 -2.190 -1.003 "C3'" 08Q 9 08Q "O3'" "O3'" O 0 1 N N N 1.989 -13.564 15.795 0.207 -3.350 -0.325 "O3'" 08Q 10 08Q "C2'" "C2'" C 0 1 N N N 2.010 -13.033 18.198 -1.819 -2.069 -0.859 "C2'" 08Q 11 08Q "C1'" "C1'" C 0 1 N N S 2.197 -11.963 19.041 -2.006 -0.535 -0.974 "C1'" 08Q 12 08Q N1 N1 N 0 1 N N N 2.331 -11.149 20.228 -3.243 -0.122 -0.307 N1 08Q 13 08Q C2 C2 C 0 1 N N N 2.252 -11.896 21.415 -4.426 -0.576 -0.758 C2 08Q 14 08Q O2 O2 O 0 1 N N N 2.176 -13.122 21.352 -4.456 -1.325 -1.715 O2 08Q 15 08Q N3 N3 N 0 1 N N N 2.294 -11.270 22.644 -5.578 -0.213 -0.164 N3 08Q 16 08Q C4 C4 C 0 1 N N N 2.378 -9.878 22.689 -5.563 0.617 0.899 C4 08Q 17 08Q N4 N4 N 0 1 N N N 3.716 -7.286 15.178 4.581 0.755 -0.786 N4 08Q 18 08Q O4 O4 O 0 1 N N N 2.424 -9.294 23.773 -6.605 0.946 1.437 O4 08Q 19 08Q C5 C5 C 0 1 N N N 2.416 -9.133 21.508 -4.325 1.103 1.383 C5 08Q 20 08Q C7 C7 C 0 1 N N N 2.510 -7.615 21.579 -4.280 2.032 2.569 C7 08Q 21 08Q C6 C6 C 0 1 N N N 2.369 -9.750 20.262 -3.184 0.718 0.771 C6 08Q 22 08Q S S S 0 1 N N N 3.024 -4.339 15.256 5.530 -1.589 2.388 S 08Q 23 08Q OP3 O1 O 0 1 N Y N 5.661 -8.938 16.688 3.323 3.007 -0.026 OP3 08Q 24 08Q H1 H1 H 0 1 N N N 4.994 -4.462 13.815 4.410 -1.716 0.261 H1 08Q 25 08Q H2 H2 H 0 1 N N N 3.667 -5.492 13.199 6.123 -1.272 0.076 H2 08Q 26 08Q H3 H3 H 0 1 N N N 5.508 -6.847 14.167 3.929 0.528 1.198 H3 08Q 27 08Q H4 H4 H 0 1 N N N 5.287 -6.003 15.738 5.643 0.972 1.014 H4 08Q 28 08Q H5 H5 H 0 1 N N N 4.553 -11.924 14.930 1.069 -0.009 -2.078 H5 08Q 29 08Q H6 H6 H 0 1 N N N 5.396 -11.127 16.352 2.180 -1.076 -1.186 H6 08Q 30 08Q H7 H7 H 0 1 N N N 4.102 -12.811 16.492 0.521 -1.123 0.712 H7 08Q 31 08Q H8 H8 H 0 1 N N N 1.311 -11.794 16.423 0.014 -2.203 -2.054 H8 08Q 32 08Q H9 H9 H 0 1 N N N 1.094 -13.882 15.774 -0.077 -4.185 -0.722 H9 08Q 33 08Q H10 H10 H 0 1 N N N 1.025 -13.489 18.379 -2.332 -2.589 -1.668 H10 08Q 34 08Q H11 H11 H 0 1 N N N 2.789 -13.790 18.370 -2.152 -2.433 0.113 H11 08Q 35 08Q H12 H12 H 0 1 N N N 1.283 -12.306 19.547 -2.020 -0.233 -2.021 H12 08Q 36 08Q H13 H13 H 0 1 N N N 2.265 -11.805 23.488 -6.423 -0.550 -0.501 H13 08Q 37 08Q H14 H14 H 0 1 N N N 3.029 -6.796 15.714 5.372 1.249 -1.171 H14 08Q 38 08Q H15 H15 H 0 1 N N N 2.537 -7.298 22.632 -5.294 2.219 2.922 H15 08Q 39 08Q H16 H16 H 0 1 N N N 3.427 -7.280 21.072 -3.695 1.574 3.367 H16 08Q 40 08Q H17 H17 H 0 1 N N N 1.634 -7.170 21.085 -3.818 2.974 2.274 H17 08Q 41 08Q H18 H18 H 0 1 N N N 2.362 -9.169 19.351 -2.229 1.075 1.129 H18 08Q 42 08Q H19 H19 H 0 1 N N N 2.589 -3.348 14.536 5.856 -2.890 2.287 H19 08Q 43 08Q HOP3 H20 H 0 0 N Y N 5.571 -9.044 17.628 3.470 2.839 0.915 HOP3 08Q 44 # 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 08Q "C8'" "C7'" SING N N 1 08Q "C8'" S SING N N 2 08Q "C7'" N4 SING N N 3 08Q N4 P SING N N 4 08Q "O5'" "C5'" SING N N 5 08Q "O5'" P SING N N 6 08Q "C5'" "C4'" SING N N 7 08Q "O3'" "C3'" SING N N 8 08Q P OP1 DOUB N N 9 08Q "C3'" "C4'" SING N N 10 08Q "C3'" "C2'" SING N N 11 08Q "C4'" "O4'" SING N N 12 08Q "O4'" "C1'" SING N N 13 08Q "C2'" "C1'" SING N N 14 08Q "C1'" N1 SING N N 15 08Q N1 C6 SING N N 16 08Q N1 C2 SING N N 17 08Q C6 C5 DOUB N N 18 08Q O2 C2 DOUB N N 19 08Q C2 N3 SING N N 20 08Q C5 C7 SING N N 21 08Q C5 C4 SING N N 22 08Q N3 C4 SING N N 23 08Q C4 O4 DOUB N N 24 08Q P OP3 SING N N 25 08Q "C8'" H1 SING N N 26 08Q "C8'" H2 SING N N 27 08Q "C7'" H3 SING N N 28 08Q "C7'" H4 SING N N 29 08Q "C5'" H5 SING N N 30 08Q "C5'" H6 SING N N 31 08Q "C4'" H7 SING N N 32 08Q "C3'" H8 SING N N 33 08Q "O3'" H9 SING N N 34 08Q "C2'" H10 SING N N 35 08Q "C2'" H11 SING N N 36 08Q "C1'" H12 SING N N 37 08Q N3 H13 SING N N 38 08Q N4 H14 SING N N 39 08Q C7 H15 SING N N 40 08Q C7 H16 SING N N 41 08Q C7 H17 SING N N 42 08Q C6 H18 SING N N 43 08Q S H19 SING N N 44 08Q OP3 HOP3 SING N N 45 # 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 08Q SMILES ACDLabs 12.01 "O=P(O)(OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O)NCCS" 08Q InChI InChI 1.03 "InChI=1S/C12H20N3O7PS/c1-7-5-15(12(18)14-11(7)17)10-4-8(16)9(22-10)6-21-23(19,20)13-2-3-24/h5,8-10,16,24H,2-4,6H2,1H3,(H2,13,19,20)(H,14,17,18)/t8-,9+,10-/m0/s1" 08Q InChIKey InChI 1.03 NNHLQGCWACQGSN-AEJSXWLSSA-N 08Q SMILES_CANONICAL CACTVS 3.370 "CC1=CN([C@@H]2C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O2)C(=O)NC1=O" 08Q SMILES CACTVS 3.370 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)NCCS)O2)C(=O)NC1=O" 08Q SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@@H]([C@H](O2)COP(=O)(NCCS)O)O" 08Q SMILES "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NCCS)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 08Q "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine" 08Q "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3S,5S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 08Q "Create component" 2011-10-15 RCSB #