data_SAY # _chem_comp.id SAY _chem_comp.name "[(2R,3S,5R)-3-hydroxy-5-(3-hydroxy-4-methanoyl-phenyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H15 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2'-DEOXY-1'-(3-HYDROXY-4-FORMYLPHENYL)RIBOSE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-11-15 _chem_comp.pdbx_modified_date 2021-03-01 _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 318.216 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SAY _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 2XY5 _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 SAY P P P 0 1 N N N 30.623 11.051 27.089 -4.282 -1.209 0.160 P SAY 1 SAY O1P O1P O 0 1 N N N 30.783 11.403 28.509 -5.438 -0.479 -0.405 O1P SAY 2 SAY O2P O2P O 0 1 N N N 30.163 9.651 26.979 -4.732 -1.965 1.509 O2P SAY 3 SAY O3P O3P O 0 1 N Y N 29.693 12.080 26.306 -3.756 -2.291 -0.911 O3P SAY 4 SAY "O5'" "O5'" O 0 1 N N N 31.948 11.188 26.215 -3.101 -0.168 0.496 "O5'" SAY 5 SAY "C5'" "C5'" C 0 1 N N N 32.113 10.239 25.162 -2.557 0.731 -0.473 "C5'" SAY 6 SAY "C4'" "C4'" C 0 1 N N R 32.916 10.774 23.963 -1.458 1.575 0.176 "C4'" SAY 7 SAY "O4'" "O4'" O 0 1 N N N 32.133 11.711 23.211 -0.346 0.737 0.534 "O4'" SAY 8 SAY "C3'" "C3'" C 0 1 N N S 34.154 11.523 24.433 -0.938 2.621 -0.830 "C3'" SAY 9 SAY "O3'" "O3'" O 0 1 N Y N 35.235 11.164 23.573 -1.141 3.942 -0.326 "O3'" SAY 10 SAY "C2'" "C2'" C 0 1 N N N 33.783 12.967 24.230 0.574 2.312 -0.951 "C2'" SAY 11 SAY "C1'" "C1'" C 0 1 N N R 32.938 12.851 22.981 0.850 1.526 0.356 "C1'" SAY 12 SAY CAA CAA C 0 1 Y N N 31.803 13.862 22.864 2.055 0.635 0.194 CAA SAY 13 SAY CAB CAB C 0 1 Y N N 31.476 14.401 21.621 3.256 0.992 0.774 CAB SAY 14 SAY CAF CAF C 0 1 Y N N 31.083 14.207 23.998 1.948 -0.541 -0.531 CAF SAY 15 SAY CAE CAE C 0 1 Y N N 30.043 15.108 23.897 3.041 -1.365 -0.687 CAE SAY 16 SAY CAD CAD C 0 1 Y N N 29.716 15.645 22.673 4.267 -1.013 -0.109 CAD SAY 17 SAY CAG CAG C 0 1 N N N 28.573 16.606 22.731 5.437 -1.885 -0.270 CAG SAY 18 SAY CAC CAC C 0 1 Y N N 30.429 15.311 21.519 4.368 0.178 0.630 CAC SAY 19 SAY OAR OAR O 0 1 N N N 30.161 15.830 20.349 5.548 0.528 1.199 OAR SAY 20 SAY OAH OAH O 0 1 N Y N 27.884 17.349 21.828 5.343 -2.914 -0.906 OAH SAY 21 SAY H2P H2P H 0 1 N N N 30.064 9.421 26.063 -5.442 -2.609 1.381 H2P SAY 22 SAY H3P H3P H 0 1 N Y N 29.508 12.827 26.863 -2.997 -2.808 -0.607 H3P SAY 23 SAY "H5'1" "H5'1" H 0 0 N N N 32.648 9.368 25.569 -2.136 0.161 -1.301 "H5'1" SAY 24 SAY "H5'2" "H5'2" H 0 0 N N N 31.108 9.990 24.792 -3.345 1.385 -0.845 "H5'2" SAY 25 SAY "H4'" "H4'" H 0 1 N N N 33.193 9.904 23.349 -1.848 2.072 1.063 "H4'" SAY 26 SAY "H3'" "H3'" H 0 1 N Y N 34.454 11.309 25.469 -1.432 2.501 -1.794 "H3'" SAY 27 SAY "H1'" "H1'" H 0 1 N N N 33.638 12.912 22.135 0.988 2.210 1.194 "H1'" SAY 28 SAY HA HA H 0 1 N N N 34.918 11.084 22.681 -0.832 4.641 -0.919 HA SAY 29 SAY "H2'1" "H2'1" H 0 0 N N N 33.227 13.387 25.081 0.777 1.696 -1.826 "H2'1" SAY 30 SAY "H2'2" "H2'2" H 0 0 N N N 34.639 13.653 24.143 1.157 3.233 -0.982 "H2'2" SAY 31 SAY HAB HAB H 0 1 N N N 32.033 14.114 20.741 3.329 1.908 1.342 HAB SAY 32 SAY HAF HAF H 0 1 N N N 31.335 13.773 24.954 1.003 -0.814 -0.977 HAF SAY 33 SAY HAE HAE H 0 1 N N N 29.486 15.392 24.778 2.953 -2.280 -1.253 HAE SAY 34 SAY HAG HAG H 0 1 N N N 28.205 16.743 23.737 6.380 -1.610 0.177 HAG SAY 35 SAY HAR HAR H 0 1 N N N 30.096 16.774 20.428 5.666 0.193 2.098 HAR SAY 36 # # 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 SAY P O1P DOUB N N 1 SAY P O2P SING N N 2 SAY P "O5'" SING N N 3 SAY P O3P SING N N 4 SAY "O5'" "C5'" SING N N 5 SAY "C5'" "C4'" SING N N 6 SAY "C4'" "O4'" SING N N 7 SAY "C4'" "C3'" SING N N 8 SAY "O4'" "C1'" SING N N 9 SAY "C3'" "O3'" SING N N 10 SAY "C3'" "C2'" SING N N 11 SAY "C2'" "C1'" SING N N 12 SAY "C1'" CAA SING N N 13 SAY CAA CAB SING Y N 14 SAY CAA CAF DOUB Y N 15 SAY CAB CAC DOUB Y N 16 SAY CAF CAE SING Y N 17 SAY CAE CAD DOUB Y N 18 SAY CAD CAG SING N N 19 SAY CAG OAH DOUB N N 20 SAY CAD CAC SING Y N 21 SAY CAC OAR SING N N 22 SAY O2P H2P SING N N 23 SAY O3P H3P SING N N 24 SAY "C5'" "H5'1" SING N N 25 SAY "C5'" "H5'2" SING N N 26 SAY "C4'" "H4'" SING N N 27 SAY "C3'" "H3'" SING N N 28 SAY "C1'" "H1'" SING N N 29 SAY "O3'" HA SING N N 30 SAY "C2'" "H2'1" SING N N 31 SAY "C2'" "H2'2" SING N N 32 SAY CAB HAB SING N N 33 SAY CAF HAF SING N N 34 SAY CAE HAE SING N N 35 SAY CAG HAG SING N N 36 SAY OAR HAR SING N N 37 # # 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 SAY SMILES_CANONICAL CACTVS 3.352 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)c2ccc(C=O)c(O)c2" SAY SMILES CACTVS 3.352 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)c2ccc(C=O)c(O)c2" SAY SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "c1cc(c(cc1[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)O)C=O" SAY SMILES "OpenEye OEToolkits" 1.6.1 "c1cc(c(cc1C2CC(C(O2)COP(=O)(O)O)O)O)C=O" SAY InChI InChI 1.03 "InChI=1S/C12H15O8P/c13-5-8-2-1-7(3-9(8)14)11-4-10(15)12(20-11)6-19-21(16,17)18/h1-3,5,10-12,14-15H,4,6H2,(H2,16,17,18)/t10-,11+,12+/m0/s1" SAY InChIKey InChI 1.03 PCWRNNXGJWWYRH-QJPTWQEYSA-N # _pdbx_chem_comp_identifier.comp_id SAY _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.6.1 _pdbx_chem_comp_identifier.identifier "[(2R,3S,5R)-3-hydroxy-5-(3-hydroxy-4-methanoyl-phenyl)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 SAY "Create component" 2010-11-15 EBI SAY "Modify aromatic_flag" 2011-06-04 RCSB SAY "Modify descriptor" 2011-06-04 RCSB SAY "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id SAY _pdbx_chem_comp_synonyms.name "2'-DEOXY-1'-(3-HYDROXY-4-FORMYLPHENYL)RIBOSE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##