data_PBT # _chem_comp.id PBT _chem_comp.name "[3-HYDROXY-5-(5-METHYL-2,4-DIOXOTETRAHYDRO-1(2H)-PYRIMIDINYL)TETRAHYDRO-2-FURANYL]METHYL DIHYDROGEN PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-10-04 _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 324.224 _chem_comp.one_letter_code N _chem_comp.three_letter_code PBT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _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 EBI # 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 PBT P P P 0 1 N N N -1.362 -7.164 2.554 -3.968 -1.665 3.118 P PBT 1 PBT O1P O1P O 0 1 N N N -2.019 -7.318 3.870 -3.912 -2.311 1.636 O1P PBT 2 PBT O2P O2P O 0 1 N Y N ? ? ? -4.901 -0.360 2.920 O2P PBT 3 PBT O3P O3P O 0 1 N Y N -0.680 -8.347 1.989 -4.406 -2.599 4.208 O3P PBT 4 PBT "O5'" O5* O 0 1 N N N -2.410 -6.632 1.455 -2.493 -1.028 3.315 "O5'" PBT 5 PBT "C5'" C5* C 0 1 N N N -3.831 -6.845 1.376 -2.005 -0.136 2.327 "C5'" PBT 6 PBT "C4'" C4* C 0 1 N N R -4.442 -6.310 0.081 -0.611 0.328 2.728 "C4'" PBT 7 PBT "O4'" O4* O 0 1 N N N -4.652 -4.857 0.165 0.247 -0.829 2.764 "O4'" PBT 8 PBT "C3'" C3* C 0 1 N N S -3.508 -6.528 -1.128 0.008 1.286 1.720 "C3'" PBT 9 PBT "O3'" O3* O 0 1 N N N -4.223 -6.976 -2.305 0.965 2.121 2.368 "O3'" PBT 10 PBT "C2'" C2* C 0 1 N N N -2.938 -5.074 -1.375 0.710 0.360 0.754 "C2'" PBT 11 PBT "C1'" C1* C 0 1 N N R -4.285 -4.325 -1.088 1.157 -0.778 1.657 "C1'" PBT 12 PBT N1 N1 N 0 1 N N N -4.399 -2.803 -1.131 1.164 -2.047 0.989 N1 PBT 13 PBT C2 C2 C 0 1 N N N -5.677 -2.367 -1.652 2.326 -2.535 0.382 C2 PBT 14 PBT O2 O2 O 0 1 N N N -6.663 -3.106 -1.767 3.415 -1.956 0.400 O2 PBT 15 PBT N3 N3 N 0 1 N N N -5.792 -1.021 -2.078 2.173 -3.767 -0.267 N3 PBT 16 PBT C4 C4 C 0 1 N N N -4.823 0.006 -1.996 1.083 -4.633 -0.213 C4 PBT 17 PBT O4 O4 O 0 1 N N N -5.092 1.165 -2.325 1.030 -5.682 -0.852 O4 PBT 18 PBT C5 C5 C 0 1 N N R -3.635 -0.302 -1.106 0.011 -4.203 0.774 C5 PBT 19 PBT C5M C5M C 0 1 N N N -2.346 0.476 -1.445 -1.324 -4.878 0.481 C5M PBT 20 PBT C6 C6 C 0 1 N N N -3.309 -1.865 -0.929 -0.124 -2.687 0.747 C6 PBT 21 PBT H1P H1P H 0 1 N N N -1.359 -7.351 4.552 -4.684 -2.823 1.313 H1P PBT 22 PBT H2P H2P H 0 1 N N N 0.422 0.099 -0.845 -5.874 -0.475 2.871 H2P PBT 23 PBT "H5'1" 1H5* H 0 0 N N N -4.295 -6.301 2.212 -1.971 -0.654 1.366 "H5'1" PBT 24 PBT "H5'2" 2H5* H 0 0 N N N -4.022 -7.927 1.428 -2.683 0.718 2.254 "H5'2" PBT 25 PBT "H4'" H4* H 0 1 N N N -5.388 -6.855 -0.052 -0.644 0.753 3.736 "H4'" PBT 26 PBT "H3'" H3* H 0 1 N N N -2.749 -7.301 -0.937 -0.722 1.941 1.236 "H3'" PBT 27 PBT HA HA H 0 1 N N N -5.145 -7.074 -2.098 1.332 2.718 1.693 HA PBT 28 PBT "H2'1" 1H2* H 0 0 N N N -2.458 -4.884 -2.346 -0.003 -0.001 0.003 "H2'1" PBT 29 PBT "H2'2" 2H2* H 0 0 N N N -2.111 -4.792 -0.706 1.556 0.818 0.232 "H2'2" PBT 30 PBT "H1'" H1* H 0 1 N N N -4.949 -4.505 -1.946 2.163 -0.604 2.054 "H1'" PBT 31 PBT H3 H3 H 0 1 N N N -6.667 -0.765 -2.488 2.965 -4.080 -0.822 H3 PBT 32 PBT H5 H5 H 0 1 N N N -3.990 0.069 -0.133 0.354 -4.523 1.766 H5 PBT 33 PBT H5M1 1H5M H 0 0 N N N -1.941 0.115 -2.402 -1.965 -4.861 1.367 H5M1 PBT 34 PBT H5M2 2H5M H 0 0 N N N -1.603 0.319 -0.649 -1.845 -4.365 -0.332 H5M2 PBT 35 PBT H5M3 3H5M H 0 0 N N N -2.575 1.549 -1.526 -1.170 -5.921 0.188 H5M3 PBT 36 PBT H6C1 1H6C H 0 0 N N N -2.582 -2.097 -1.721 -0.484 -2.336 -0.228 H6C1 PBT 37 PBT H6C2 2H6C H 0 0 N N N -2.956 -2.003 0.104 -0.829 -2.358 1.519 H6C2 PBT 38 # 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 PBT P O1P SING N N 1 PBT P O2P SING N N 2 PBT P O3P DOUB N N 3 PBT P "O5'" SING N N 4 PBT O1P H1P SING N N 5 PBT O2P H2P SING N N 6 PBT "O5'" "C5'" SING N N 7 PBT "C5'" "C4'" SING N N 8 PBT "C5'" "H5'1" SING N N 9 PBT "C5'" "H5'2" SING N N 10 PBT "C4'" "O4'" SING N N 11 PBT "C4'" "C3'" SING N N 12 PBT "C4'" "H4'" SING N N 13 PBT "O4'" "C1'" SING N N 14 PBT "C3'" "O3'" SING N N 15 PBT "C3'" "C2'" SING N N 16 PBT "C3'" "H3'" SING N N 17 PBT "O3'" HA SING N N 18 PBT "C2'" "C1'" SING N N 19 PBT "C2'" "H2'1" SING N N 20 PBT "C2'" "H2'2" SING N N 21 PBT "C1'" N1 SING N N 22 PBT "C1'" "H1'" SING N N 23 PBT N1 C2 SING N N 24 PBT N1 C6 SING N N 25 PBT C2 O2 DOUB N N 26 PBT C2 N3 SING N N 27 PBT N3 C4 SING N N 28 PBT N3 H3 SING N N 29 PBT C4 O4 DOUB N N 30 PBT C4 C5 SING N N 31 PBT C5 C5M SING N N 32 PBT C5 C6 SING N N 33 PBT C5 H5 SING N N 34 PBT C5M H5M1 SING N N 35 PBT C5M H5M2 SING N N 36 PBT C5M H5M3 SING N N 37 PBT C6 H6C1 SING N N 38 PBT C6 H6C2 SING N N 39 # 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 PBT SMILES ACDLabs 10.04 "O=C1N(CC(C(=O)N1)C)C2OC(C(O)C2)COP(=O)(O)O" PBT SMILES_CANONICAL CACTVS 3.341 "C[C@@H]1CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" PBT SMILES CACTVS 3.341 "C[CH]1CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" PBT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H]1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" PBT SMILES "OpenEye OEToolkits" 1.5.0 "CC1CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" PBT InChI InChI 1.03 "InChI=1S/C10H17N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h5-8,13H,2-4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,7-,8-/m1/s1" PBT InChIKey InChI 1.03 PGRQANKWVMVANW-ULAWRXDQSA-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 PBT "SYSTEMATIC NAME" ACDLabs 10.04 ;5'-thymidylic acid ; PBT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-[(5R)-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]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 PBT "Create component" 2001-10-04 EBI PBT "Modify descriptor" 2011-06-04 RCSB #