data_XTR # _chem_comp.id XTR _chem_comp.name "[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-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 2009-01-05 _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 HDP _chem_comp.formula_weight 332.246 _chem_comp.one_letter_code T _chem_comp.three_letter_code XTR _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 3FL6 _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 XTR OP3 O3P O 0 1 N Y N 20.825 39.982 30.214 -5.512 0.209 -1.373 OP3 XTR 1 XTR "C4'" "C4'" C 0 1 N N R 23.416 38.455 28.045 -1.052 -1.397 0.225 "C4'" XTR 2 XTR "C7'" "C7'" C 0 1 N N N 22.201 36.500 29.020 0.661 -1.453 -1.555 "C7'" XTR 3 XTR "C6'" "C6'" C 0 1 N N N 22.898 37.634 29.192 -0.570 -1.284 -1.192 "C6'" XTR 4 XTR "C1'" "C1'" C 0 1 N N S 21.830 35.947 27.668 1.780 -1.774 -0.609 "C1'" XTR 5 XTR O4 O4 O 0 1 N N N 16.787 34.005 28.587 4.770 2.638 0.261 O4 XTR 6 XTR C4 C4 C 0 1 N N N 17.886 34.502 28.379 4.088 1.647 0.067 C4 XTR 7 XTR C5 C5 C 0 1 N N N 18.127 35.908 28.154 2.681 1.711 0.203 C5 XTR 8 XTR C5M C5M C 0 1 N N N 16.974 36.860 28.176 2.008 3.003 0.588 C5M XTR 9 XTR C6 C6 C 0 1 N N N 19.390 36.279 27.942 1.948 0.598 -0.019 C6 XTR 10 XTR N3 N3 N 0 1 N N N 19.008 33.704 28.335 4.667 0.481 -0.284 N3 XTR 11 XTR C2 C2 C 0 1 N N N 20.313 34.076 28.119 3.913 -0.613 -0.499 C2 XTR 12 XTR O2 O2 O 0 1 N N N 21.215 33.251 28.111 4.449 -1.658 -0.815 O2 XTR 13 XTR N1 N1 N 0 1 N N N 20.478 35.431 27.915 2.575 -0.567 -0.369 N1 XTR 14 XTR "C2'" "C2'" C 0 1 N N N 21.909 36.975 26.530 1.217 -2.283 0.720 "C2'" XTR 15 XTR "C3'" "C3'" C 0 1 N N S 23.177 37.693 26.761 0.131 -1.309 1.192 "C3'" XTR 16 XTR P P P 0 1 N N N 21.673 41.251 29.700 -4.439 0.612 -0.242 P XTR 17 XTR OP1 O1P O 0 1 N N N 22.204 42.048 30.839 -3.955 1.988 -0.489 OP1 XTR 18 XTR OP2 O2P O 0 1 N N N 20.754 41.858 28.709 -5.136 0.540 1.208 OP2 XTR 19 XTR "O5'" "O5'" O 0 1 N N N 22.935 40.620 28.978 -3.197 -0.411 -0.291 "O5'" XTR 20 XTR "C5'" "C5'" C 0 1 N N N 22.655 39.737 27.896 -2.030 -0.258 0.520 "C5'" XTR 21 XTR "O3'" "O3'" O 0 1 N N N 24.193 36.755 26.384 -0.297 -1.667 2.507 "O3'" XTR 22 XTR HOP3 HO3P H 0 0 N N N 20.658 39.396 29.485 -6.289 0.784 -1.401 HO3P XTR 23 XTR "H4'" "H4'" H 0 1 N N N 24.479 38.660 28.240 -1.558 -2.353 0.359 "H4'" XTR 24 XTR "H7'" "H7'" H 0 1 N N N 21.889 35.954 29.898 0.897 -1.356 -2.605 "H7'" XTR 25 XTR "H6'" "H6'" H 0 1 N N N 23.095 37.971 30.199 -1.296 -1.049 -1.957 "H6'" XTR 26 XTR "H1'" "H1'" H 0 1 N N N 22.529 35.179 27.304 2.416 -2.543 -1.048 "H1'" XTR 27 XTR H5M H5M H 0 1 N N N 16.711 37.094 29.218 2.762 3.780 0.721 H5M XTR 28 XTR H5MA H5MA H 0 0 N N N 17.253 37.786 27.652 1.315 3.301 -0.199 H5MA XTR 29 XTR H5MB H5MB H 0 0 N N N 16.110 36.400 27.674 1.461 2.865 1.520 H5MB XTR 30 XTR H6 H6 H 0 1 N N N 19.577 37.330 27.778 0.873 0.628 0.080 H6 XTR 31 XTR HN3 HN3 H 0 1 N N N 18.853 32.727 28.479 5.631 0.430 -0.382 HN3 XTR 32 XTR "H2'" "H2'" H 0 1 N N N 21.908 36.479 25.548 0.785 -3.274 0.579 "H2'" XTR 33 XTR "H2'A" "H2'A" H 0 0 N N N 21.044 37.654 26.525 2.015 -2.331 1.462 "H2'A" XTR 34 XTR "H3'" "H3'" H 0 1 N N N 23.166 38.605 26.146 0.526 -0.293 1.196 "H3'" XTR 35 XTR "H5'" "H5'" H 0 1 N N N 22.949 40.221 26.953 -2.313 -0.285 1.572 "H5'" XTR 36 XTR "H5'A" "H5'A" H 0 0 N N N 21.579 39.511 27.894 -1.555 0.697 0.296 "H5'A" XTR 37 XTR "HO3'" "HO3'" H 0 0 N Y N 24.106 36.547 25.461 0.408 -1.648 3.169 "HO3'" XTR 38 XTR HOP2 HO2P H 0 0 N N N 19.901 41.988 29.106 -5.478 -0.335 1.438 HO2P XTR 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 XTR OP3 HOP3 SING N N 1 XTR "C4'" "C6'" SING N N 2 XTR "C4'" "H4'" SING N N 3 XTR "C7'" "C6'" DOUB N N 4 XTR "C7'" "H7'" SING N N 5 XTR "C6'" "H6'" SING N N 6 XTR "C1'" "C7'" SING N N 7 XTR "C1'" N1 SING N N 8 XTR "C1'" "H1'" SING N N 9 XTR C4 O4 DOUB N N 10 XTR C5 C4 SING N N 11 XTR C5 C5M SING N N 12 XTR C5M H5M SING N N 13 XTR C5M H5MA SING N N 14 XTR C5M H5MB SING N N 15 XTR C6 C5 DOUB N N 16 XTR C6 H6 SING N N 17 XTR N3 C4 SING N N 18 XTR N3 HN3 SING N N 19 XTR C2 N3 SING N N 20 XTR O2 C2 DOUB N N 21 XTR N1 C6 SING N N 22 XTR N1 C2 SING N N 23 XTR "C2'" "C1'" SING N N 24 XTR "C2'" "C3'" SING N N 25 XTR "C2'" "H2'" SING N N 26 XTR "C2'" "H2'A" SING N N 27 XTR "C3'" "C4'" SING N N 28 XTR "C3'" "H3'" SING N N 29 XTR P OP3 SING N N 30 XTR P OP1 DOUB N N 31 XTR OP2 P SING N N 32 XTR "O5'" P SING N N 33 XTR "C5'" "C4'" SING N N 34 XTR "C5'" "O5'" SING N N 35 XTR "C5'" "H5'" SING N N 36 XTR "C5'" "H5'A" SING N N 37 XTR "O3'" "C3'" SING N N 38 XTR "O3'" "HO3'" SING N N 39 XTR OP2 HOP2 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 XTR SMILES ACDLabs 10.04 "O=P(O)(O)OCC2C=CC(N1C=C(C(=O)NC1=O)C)CC2O" XTR 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" XTR SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)C=C2)C(=O)NC1=O" XTR 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" XTR SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(C=C2)COP(=O)(O)O)O" XTR 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+/m1/s1" XTR InChIKey InChI 1.03 PIQIDTLVJACCCC-BBBLOLIVSA-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 XTR "SYSTEMATIC NAME" ACDLabs 10.04 "[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate" XTR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R,4S,6S)-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 XTR "Create component" 2009-01-05 RCSB XTR "Modify descriptor" 2011-06-04 RCSB #