data_XTL # _chem_comp.id XTL _chem_comp.name "[(1S,4R,6R)-6-HYDROXY-4-(THYMIN-9-YL)CYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H17 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-05-19 _chem_comp.pdbx_modified_date 2011-06-04 _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 332.246 _chem_comp.one_letter_code T _chem_comp.three_letter_code XTL _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 XTL P P P 0 1 N N N -0.407 -5.216 23.991 -4.265 -0.636 -0.217 P XTL 1 XTL OP1 O1P O 0 1 N N N -1.012 -4.789 25.244 -3.568 -1.930 -0.395 OP1 XTL 2 XTL OP2 O2P O 0 1 N N N 0.234 -6.531 23.924 -4.816 -0.527 1.291 OP2 XTL 3 XTL "O5'" O5* O 0 1 N N N 0.744 -4.126 23.566 -3.237 0.570 -0.502 "O5'" XTL 4 XTL "C5'" C5* C 0 1 N N N 0.619 -2.739 23.950 -2.114 0.368 0.358 "C5'" XTL 5 XTL "C4'" C4* C 0 1 N N S 1.732 -1.908 23.379 -1.094 1.486 0.137 "C4'" XTL 6 XTL "C6'" C6* C 0 1 N N N 1.569 -1.904 21.931 -0.561 1.400 -1.263 "C6'" XTL 7 XTL "C7'" C7* C 0 1 N N N 2.488 -1.996 20.971 0.685 1.543 -1.573 "C7'" XTL 8 XTL "C3'" C3* C 0 1 N N R 3.108 -2.507 23.767 0.048 1.338 1.145 "C3'" XTL 9 XTL "O3'" O3* O 0 1 N N N 3.316 -2.075 25.097 -0.417 1.668 2.455 "O3'" XTL 10 XTL "C2'" C2* C 0 1 N N N 4.157 -1.875 22.864 1.178 2.294 0.742 "C2'" XTL 11 XTL "C1'" C1* C 0 1 N N R 3.954 -2.281 21.373 1.777 1.807 -0.578 "C1'" XTL 12 XTL C6 C6 C 0 1 N N N 3.646 -4.740 21.401 1.859 -0.584 -0.048 C6 XTL 13 XTL C5 C5 C 0 1 N N N 4.084 -6.001 21.265 2.552 -1.723 0.168 C5 XTL 14 XTL C5M C5M C 0 1 N N N 3.160 -7.177 21.475 1.831 -3.005 0.495 C5M XTL 15 XTL C4 C4 C 0 1 N N N 5.464 -6.235 20.912 3.965 -1.694 0.089 C4 XTL 16 XTL O4 O4 O 0 1 N N N 5.973 -7.347 20.761 4.612 -2.708 0.280 O4 XTL 17 XTL N3 N3 N 0 1 N N N 6.208 -5.097 20.747 4.588 -0.536 -0.209 N3 XTL 18 XTL C2 C2 C 0 1 N N N 5.809 -3.797 20.874 3.872 0.584 -0.420 C2 XTL 19 XTL O2 O2 O 0 1 N N N 6.551 -2.838 20.706 4.448 1.622 -0.684 O2 XTL 20 XTL N1 N1 N 0 1 N N N 4.485 -3.674 21.211 2.529 0.572 -0.344 N1 XTL 21 XTL OP3 O3P O 0 1 N Y N -1.530 -5.309 23.127 -5.498 -0.545 -1.248 OP3 XTL 22 XTL HOP2 2HOP H 0 0 N N N 0.373 -6.770 23.015 -5.262 0.329 1.364 HOP2 XTL 23 XTL "H5'" 1H5* H 0 1 N N N 0.668 -2.677 25.047 -1.653 -0.594 0.134 "H5'" XTL 24 XTL "H5''" 2H5* H 0 0 N N N -0.340 -2.352 23.576 -2.445 0.378 1.397 "H5''" XTL 25 XTL "H4'" H4* H 0 1 N N N 1.694 -0.883 23.776 -1.579 2.451 0.280 "H4'" XTL 26 XTL "H6'" H6* H 0 1 N N N 0.550 -1.813 21.584 -1.263 1.205 -2.061 "H6'" XTL 27 XTL "H7'" H7* H 0 1 N N N 2.215 -1.874 19.933 0.959 1.470 -2.615 "H7'" XTL 28 XTL "H3'" H3* H 0 1 N N N 3.159 -3.602 23.671 0.416 0.312 1.134 "H3'" XTL 29 XTL "HO3'" H3T H 0 0 N Y N 3.363 -2.830 25.672 0.339 1.575 3.051 "HO3'" XTL 30 XTL "H2'" 1H2* H 0 1 N N N 5.147 -2.230 23.186 1.947 2.298 1.515 "H2'" XTL 31 XTL "H2''" 2H2* H 0 0 N N N 4.081 -0.781 22.946 0.778 3.300 0.614 "H2''" XTL 32 XTL "H1'" H1* H 0 1 N N N 4.526 -1.684 20.647 2.449 2.569 -0.974 "H1'" XTL 33 XTL H6 H6 H 0 1 N N N 2.614 -4.562 21.665 0.780 -0.586 0.011 H6 XTL 34 XTL H71 1H5M H 0 1 N N N 2.225 -6.830 21.940 1.601 -3.538 -0.428 H71 XTL 35 XTL H72 2H5M H 0 1 N N N 3.646 -7.912 22.133 2.465 -3.627 1.126 H72 XTL 36 XTL H73 3H5M H 0 1 N N N 2.935 -7.645 20.505 0.905 -2.777 1.023 H73 XTL 37 XTL HN3 HN3 H 0 1 N N N 7.167 -5.236 20.502 5.556 -0.509 -0.268 HN3 XTL 38 XTL HOP3 3HOP H 0 0 N N N -2.327 -5.330 23.644 -6.088 -1.283 -1.044 HOP3 XTL 39 # 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 XTL P OP1 DOUB N N 1 XTL P OP2 SING N N 2 XTL P "O5'" SING N N 3 XTL P OP3 SING N N 4 XTL OP2 HOP2 SING N N 5 XTL "O5'" "C5'" SING N N 6 XTL "C5'" "C4'" SING N N 7 XTL "C5'" "H5'" SING N N 8 XTL "C5'" "H5''" SING N N 9 XTL "C4'" "C6'" SING N N 10 XTL "C4'" "C3'" SING N N 11 XTL "C4'" "H4'" SING N N 12 XTL "C6'" "C7'" DOUB N N 13 XTL "C6'" "H6'" SING N N 14 XTL "C7'" "C1'" SING N N 15 XTL "C7'" "H7'" SING N N 16 XTL "C3'" "O3'" SING N N 17 XTL "C3'" "C2'" SING N N 18 XTL "C3'" "H3'" SING N N 19 XTL "O3'" "HO3'" SING N N 20 XTL "C2'" "C1'" SING N N 21 XTL "C2'" "H2'" SING N N 22 XTL "C2'" "H2''" SING N N 23 XTL "C1'" N1 SING N N 24 XTL "C1'" "H1'" SING N N 25 XTL C6 C5 DOUB N N 26 XTL C6 N1 SING N N 27 XTL C6 H6 SING N N 28 XTL C5 C5M SING N N 29 XTL C5 C4 SING N N 30 XTL C5M H71 SING N N 31 XTL C5M H72 SING N N 32 XTL C5M H73 SING N N 33 XTL C4 O4 DOUB N N 34 XTL C4 N3 SING N N 35 XTL N3 C2 SING N N 36 XTL N3 HN3 SING N N 37 XTL C2 O2 DOUB N N 38 XTL C2 N1 SING N N 39 XTL OP3 HOP3 SING N N 40 # 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 XTL SMILES ACDLabs 10.04 "O=P(O)(O)OCC2C=CC(N1C=C(C(=O)NC1=O)C)CC2O" XTL SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2C[C@@H](O)[C@H](CO[P](O)(O)=O)C=C2)C(=O)NC1=O" XTL SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)C=C2)C(=O)NC1=O" XTL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](C=C2)COP(=O)(O)O)O" XTL SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(C=C2)COP(=O)(O)O)O" XTL InChI InChI 1.03 "InChI=1S/C12H17N2O7P/c1-7-5-14(12(17)13-11(7)16)9-3-2-8(10(15)4-9)6-21-22(18,19)20/h2-3,5,8-10,15H,4,6H2,1H3,(H,13,16,17)(H2,18,19,20)/t8-,9-,10+/m0/s1" XTL InChIKey InChI 1.03 PIQIDTLVJACCCC-LPEHRKFASA-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 XTL "SYSTEMATIC NAME" ACDLabs 10.04 "[(1S,4R,6R)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate" XTL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1S,4R,6R)-6-hydroxy-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-1-cyclohex-2-enyl]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 XTL "Create component" 2006-05-19 RCSB XTL "Modify descriptor" 2011-06-04 RCSB #