data_5PY # _chem_comp.id 5PY _chem_comp.name "1-(2'-DEOXY-5'-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 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 2006-10-12 _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 306.209 _chem_comp.one_letter_code T _chem_comp.three_letter_code 5PY _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 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 5PY P P P 0 1 N N N 20.049 5.359 53.620 -3.968 -1.665 3.118 P 5PY 1 5PY OP2 O2P O 0 1 N N N 19.790 4.980 52.234 -3.912 -2.311 1.636 OP2 5PY 2 5PY OP1 O1P O 0 1 N N N 19.043 5.020 54.628 -4.406 -2.599 4.208 OP1 5PY 3 5PY "O5'" O5* O 0 1 N N N 21.432 4.574 53.729 -2.493 -1.028 3.315 "O5'" 5PY 4 5PY "C5'" C5* C 0 1 N N N 22.401 4.741 54.638 -2.005 -0.136 2.327 "C5'" 5PY 5 5PY "C4'" C4* C 0 1 N N R 23.503 5.614 54.058 -0.611 0.328 2.728 "C4'" 5PY 6 5PY "O4'" O4* O 0 1 N N N 24.028 6.186 55.262 0.247 -0.829 2.764 "O4'" 5PY 7 5PY "C1'" C1* C 0 1 N N R 25.423 5.949 55.303 1.157 -0.778 1.657 "C1'" 5PY 8 5PY N1 N1 N 0 1 N N N 25.841 5.862 56.718 1.164 -2.047 0.989 N1 5PY 9 5PY C2 C2 C 0 1 N N N 27.201 5.715 56.962 2.333 -2.557 0.365 C2 5PY 10 5PY O2 O2 O 0 1 N N N 28.020 5.609 56.065 3.389 -1.922 0.376 O2 5PY 11 5PY N3 N3 N 0 1 N N N 27.527 5.659 58.299 2.265 -3.790 -0.263 N3 5PY 12 5PY C4 C4 C 0 1 N N N 26.660 5.780 59.359 1.144 -4.433 -0.261 C4 5PY 13 5PY C5 C5 C 0 1 N N N 25.264 5.988 59.046 -0.110 -3.975 0.360 C5 5PY 14 5PY C5M C5M C 0 1 N N N 24.292 6.282 60.145 -1.326 -4.827 0.280 C5M 5PY 15 5PY C6 C6 C 0 1 N N N 24.915 6.019 57.747 -0.014 -2.785 0.958 C6 5PY 16 5PY "C2'" C2* C 0 1 N N N 25.684 4.690 54.469 0.710 0.360 0.754 "C2'" 5PY 17 5PY "C3'" C3* C 0 1 N N S 24.697 4.971 53.339 0.008 1.286 1.720 "C3'" 5PY 18 5PY "O3'" O3* O 0 1 N N N 25.298 5.911 52.415 0.965 2.121 2.368 "O3'" 5PY 19 5PY OP3 O3P O 0 1 N Y N ? ? ? -4.901 -0.360 2.920 OP3 5PY 20 5PY H71 1H5M H 0 1 N N N 24.830 6.354 61.102 -2.065 -4.366 -0.379 H71 5PY 21 5PY H72 2H5M H 0 1 N N N 23.782 7.235 59.938 -1.765 -4.953 1.272 H72 5PY 22 5PY H73 3H5M H 0 1 N N N 23.549 5.473 60.203 -1.069 -5.814 -0.113 H73 5PY 23 5PY H4 H4 H 0 1 N N N 27.006 5.722 60.380 1.099 -5.414 -0.763 H4 5PY 24 5PY H6 H6 H 0 1 N N N 23.877 6.172 57.492 -0.865 -2.330 1.454 H6 5PY 25 5PY "H1'" H1* H 0 1 N N N 26.027 6.758 54.867 2.163 -0.604 2.054 "H1'" 5PY 26 5PY "H2'" 1H2* H 0 1 N N N 26.726 4.599 54.128 -0.003 -0.001 0.003 "H2'" 5PY 27 5PY "H2''" 2H2* H 0 0 N N N 25.549 3.733 54.994 1.556 0.818 0.232 "H2''" 5PY 28 5PY "H3'" H3* H 0 1 N N N 24.411 4.079 52.763 -0.722 1.941 1.236 "H3'" 5PY 29 5PY "HO3'" H3T H 0 0 N Y N 25.430 6.745 52.851 0.743 3.042 2.146 "HO3'" 5PY 30 5PY "H4'" H4* H 0 1 N N N 23.062 6.238 53.266 -0.644 0.753 3.736 "H4'" 5PY 31 5PY "H5'" 1H5* H 0 1 N N N 21.983 5.226 55.532 -1.971 -0.654 1.366 "H5'" 5PY 32 5PY "H5''" 2H5* H 0 0 N N N 22.818 3.760 54.910 -2.683 0.718 2.254 "H5''" 5PY 33 5PY HOP2 2HOP H 0 0 N N N 19.734 5.761 51.697 -4.684 -2.823 1.313 HOP2 5PY 34 5PY HOP3 3HOP H 0 0 N N N ? ? ? -5.874 -0.475 2.871 HOP3 5PY 35 # 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 5PY P "O5'" SING N N 1 5PY P OP2 SING N N 2 5PY P OP3 SING N N 3 5PY P OP1 DOUB N N 4 5PY OP2 HOP2 SING N N 5 5PY "O5'" "C5'" SING N N 6 5PY "C5'" "C4'" SING N N 7 5PY "C5'" "H5'" SING N N 8 5PY "C5'" "H5''" SING N N 9 5PY "C4'" "C3'" SING N N 10 5PY "C4'" "O4'" SING N N 11 5PY "C4'" "H4'" SING N N 12 5PY "O4'" "C1'" SING N N 13 5PY "C1'" N1 SING N N 14 5PY "C1'" "C2'" SING N N 15 5PY "C1'" "H1'" SING N N 16 5PY N1 C2 SING N N 17 5PY N1 C6 SING N N 18 5PY C2 N3 SING N N 19 5PY C2 O2 DOUB N N 20 5PY N3 C4 DOUB N N 21 5PY C4 C5 SING N N 22 5PY C4 H4 SING N N 23 5PY C5 C5M SING N N 24 5PY C5 C6 DOUB N N 25 5PY C5M H71 SING N N 26 5PY C5M H72 SING N N 27 5PY C5M H73 SING N N 28 5PY C6 H6 SING N N 29 5PY "C2'" "C3'" SING N N 30 5PY "C2'" "H2'" SING N N 31 5PY "C2'" "H2''" SING N N 32 5PY "C3'" "O3'" SING N N 33 5PY "C3'" "H3'" SING N N 34 5PY "O3'" "HO3'" SING N N 35 5PY OP3 HOP3 SING N N 36 # 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 5PY SMILES ACDLabs 10.04 "O=P(O)(O)OCC2OC(N1C(=O)N=CC(=C1)C)CC2O" 5PY SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1" 5PY SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1" 5PY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 5PY SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1)C2CC(C(O2)COP(=O)(O)O)O" 5PY InChI InChI 1.03 "InChI=1S/C10H15N2O7P/c1-6-3-11-10(14)12(4-6)9-2-7(13)8(19-9)5-18-20(15,16)17/h3-4,7-9,13H,2,5H2,1H3,(H2,15,16,17)/t7-,8+,9+/m0/s1" 5PY InChIKey InChI 1.03 TWYWJJKQSULVQX-DJLDLDEBSA-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 5PY "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methylpyrimidin-2(1H)-one" 5PY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2-oxo-pyrimidin-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 5PY "Create component" 2006-10-12 RCSB 5PY "Modify descriptor" 2011-06-04 RCSB #