data_T48 # _chem_comp.id T48 _chem_comp.name ;6'-ALPHA-HYDROXY CARBOCYCLIC THYMIDINE 5'-MONOPHOSPHATE ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1996-12-07 _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 336.235 _chem_comp.one_letter_code T _chem_comp.three_letter_code T48 _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 291D _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 T48 O3P O3P O 0 1 N Y N 8.665 12.655 11.234 0.127 0.443 -5.963 O3P T48 1 T48 P P P 0 1 N N N 8.057 13.772 12.008 0.657 -0.099 -4.543 P T48 2 T48 O1P O1P O 0 1 N N N 6.774 13.631 12.710 1.083 -1.510 -4.681 O1P T48 3 T48 O2P O2P O 0 1 N N N 9.148 14.343 12.954 1.906 0.793 -4.060 O2P T48 4 T48 "O5'" O5* O 0 1 N N N 7.945 15.002 11.041 -0.525 -0.000 -3.455 "O5'" T48 5 T48 "C5'" C5* C 0 1 N N N 7.203 16.158 11.389 0.003 -0.493 -2.223 "C5'" T48 6 T48 "C4'" C4* C 0 1 N N R 7.458 17.254 10.351 -1.075 -0.426 -1.141 "C4'" T48 7 T48 "C3'" C3* C 0 1 N N S 7.120 16.769 8.925 -1.511 1.032 -0.921 "C3'" T48 8 T48 "O3'" O3* O 0 1 N N N 6.639 17.844 8.206 -2.913 1.167 -1.163 "O3'" T48 9 T48 "C2'" C2* C 0 1 N N N 8.436 16.513 8.270 -1.194 1.370 0.549 "C2'" T48 10 T48 "C1'" C1* C 0 1 N N S 9.248 17.608 8.836 -1.172 -0.005 1.259 "C1'" T48 11 T48 N1 N1 N 0 1 N N N 10.663 17.457 8.550 -0.364 0.051 2.479 N1 T48 12 T48 C2 C2 C 0 1 N N N 11.309 18.642 8.166 0.916 0.458 2.412 C2 T48 13 T48 O2 O2 O 0 1 N N N 10.717 19.725 8.045 1.389 0.773 1.337 O2 T48 14 T48 N3 N3 N 0 1 N N N 12.660 18.526 7.892 1.681 0.521 3.517 N3 T48 15 T48 C4 C4 C 0 1 N N N 13.383 17.372 7.972 1.171 0.179 4.718 C4 T48 16 T48 O4 O4 O 0 1 N N N 14.584 17.425 7.720 1.862 0.236 5.718 O4 T48 17 T48 C5 C5 C 0 1 N N N 12.626 16.200 8.376 -0.173 -0.254 4.802 C5 T48 18 T48 C5M C5M C 0 1 N N N 13.349 14.875 8.518 -0.767 -0.645 6.131 C5M T48 19 T48 C C C 0 1 N N S 8.951 17.523 10.311 -0.510 -0.928 0.205 C T48 20 T48 C6 C6 C 0 1 N N N 11.321 16.264 8.649 -0.918 -0.307 3.678 C6 T48 21 T48 O O O 0 1 N N N 9.371 18.644 11.136 -0.874 -2.293 0.423 O T48 22 T48 H3P H3P H 0 1 N N N 9.494 12.746 10.780 0.864 0.366 -6.584 H3P T48 23 T48 H2P H2P H 0 1 N N N 8.760 15.055 13.447 1.587 1.702 -3.982 H2P T48 24 T48 "H5'1" 1H5* H 0 0 N N N 7.418 16.501 12.428 0.856 0.116 -1.924 "H5'1" T48 25 T48 "H5'2" 2H5* H 0 0 N N N 6.117 15.941 11.516 0.324 -1.527 -2.353 "H5'2" T48 26 T48 "H4'" H4* H 0 1 N N N 6.892 18.181 10.602 -1.933 -1.032 -1.432 "H4'" T48 27 T48 "H3'" H3* H 0 1 N N N 6.439 15.886 8.908 -0.953 1.693 -1.585 "H3'" T48 28 T48 HA HA H 0 1 N N N 6.431 17.545 7.328 -3.139 2.091 -0.991 HA T48 29 T48 "H2'1" 1H2* H 0 0 N N N 8.415 16.458 7.157 -1.973 2.005 0.972 "H2'1" T48 30 T48 "H2'2" 2H2* H 0 0 N N N 8.850 15.487 8.410 -0.221 1.855 0.628 "H2'2" T48 31 T48 "H1'" H1* H 0 1 N N N 8.888 18.585 8.438 -2.185 -0.340 1.484 "H1'" T48 32 T48 H3 H3 H 0 1 N N N 13.155 19.371 7.607 2.603 0.816 3.451 H3 T48 33 T48 H5M1 1H5M H 0 0 N N N 14.439 14.821 8.290 -0.014 -0.536 6.912 H5M1 T48 34 T48 H5M2 2H5M H 0 0 N N N 12.818 14.111 7.904 -1.617 -0.001 6.353 H5M2 T48 35 T48 H5M3 3H5M H 0 0 N N N 13.180 14.484 9.549 -1.099 -1.683 6.089 H5M3 T48 36 T48 H H H 0 1 N N N 9.463 16.613 10.701 0.572 -0.814 0.231 H T48 37 T48 H6 H6 H 0 1 N N N 10.775 15.355 8.954 -1.947 -0.632 3.723 H6 T48 38 T48 HB HB H 0 1 N N N 10.306 18.812 11.111 -0.496 -2.550 1.275 HB T48 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 T48 O3P P SING N N 1 T48 O3P H3P SING N N 2 T48 P O1P DOUB N N 3 T48 P O2P SING N N 4 T48 P "O5'" SING N N 5 T48 O2P H2P SING N N 6 T48 "O5'" "C5'" SING N N 7 T48 "C5'" "C4'" SING N N 8 T48 "C5'" "H5'1" SING N N 9 T48 "C5'" "H5'2" SING N N 10 T48 "C4'" "C3'" SING N N 11 T48 "C4'" C SING N N 12 T48 "C4'" "H4'" SING N N 13 T48 "C3'" "O3'" SING N N 14 T48 "C3'" "C2'" SING N N 15 T48 "C3'" "H3'" SING N N 16 T48 "O3'" HA SING N N 17 T48 "C2'" "C1'" SING N N 18 T48 "C2'" "H2'1" SING N N 19 T48 "C2'" "H2'2" SING N N 20 T48 "C1'" N1 SING N N 21 T48 "C1'" C SING N N 22 T48 "C1'" "H1'" SING N N 23 T48 N1 C2 SING N N 24 T48 N1 C6 SING N N 25 T48 C2 O2 DOUB N N 26 T48 C2 N3 SING N N 27 T48 N3 C4 SING N N 28 T48 N3 H3 SING N N 29 T48 C4 O4 DOUB N N 30 T48 C4 C5 SING N N 31 T48 C5 C5M SING N N 32 T48 C5 C6 DOUB N N 33 T48 C5M H5M1 SING N N 34 T48 C5M H5M2 SING N N 35 T48 C5M H5M3 SING N N 36 T48 C O SING N N 37 T48 C H SING N N 38 T48 C6 H6 SING N N 39 T48 O HB 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 T48 SMILES ACDLabs 10.04 "O=P(O)(O)OCC2C(O)C(N1C=C(C(=O)NC1=O)C)CC2O" T48 SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)[C@@H]2O)C(=O)NC1=O" T48 SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)[CH]2O)C(=O)NC1=O" T48 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H]([C@@H]2O)COP(=O)(O)O)O" T48 SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(C2O)COP(=O)(O)O)O" T48 InChI InChI 1.03 "InChI=1S/C11H17N2O8P/c1-5-3-13(11(17)12-10(5)16)7-2-8(14)6(9(7)15)4-21-22(18,19)20/h3,6-9,14-15H,2,4H2,1H3,(H,12,16,17)(H2,18,19,20)/t6-,7+,8+,9+/m1/s1" T48 InChIKey InChI 1.03 XBCGTBYCRNQMDB-XGEHTFHBSA-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 T48 "SYSTEMATIC NAME" ACDLabs 10.04 "[(1R,2S,3S,5S)-2,5-dihydroxy-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]methyl dihydrogen phosphate" T48 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R,2S,3S,5S)-2,5-dihydroxy-3-(5-methyl-2,4-dioxo-pyrimidin-1-yl)cyclopentyl]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 T48 "Create component" 1996-12-07 PDBJ T48 "Modify descriptor" 2011-06-04 RCSB #