data_DPY # _chem_comp.id DPY _chem_comp.name ;2-DEOXYRIBOFURANOSYL-PYRIDINE-2,6-DICARBOXYLIC ACID-5'-MONOPHOSPHATE ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H14 N O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-06-25 _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 363.214 _chem_comp.one_letter_code N _chem_comp.three_letter_code DPY _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 DPY P P P 0 1 N N N 25.511 6.049 26.189 4.581 -4.208 2.354 P DPY 1 DPY O1P O1P O 0 1 N N N 24.621 5.691 25.042 4.705 -5.662 2.004 O1P DPY 2 DPY O2P O2P O 0 1 N N N 26.937 6.347 25.921 4.410 -3.887 3.929 O2P DPY 3 DPY "O5'" O5* O 0 1 N N N 24.851 7.290 26.925 3.329 -3.444 1.668 "O5'" DPY 4 DPY C1 C1 C 0 1 Y N N 25.304 9.776 30.527 -1.069 -1.322 2.936 C1 DPY 5 DPY C2 C2 C 0 1 Y N N 26.013 10.316 31.604 -2.437 -1.127 3.059 C2 DPY 6 DPY C7 C7 C 0 1 N N N 27.051 11.268 31.456 -3.287 -1.000 1.884 C7 DPY 7 DPY O71 O71 O 0 1 N N N 27.420 11.705 30.380 -2.936 -0.536 0.795 O71 DPY 8 DPY O72 O72 O 0 1 N N N 27.573 11.646 32.528 -4.549 -1.457 2.105 O72 DPY 9 DPY N3 N3 N 0 1 Y N N 25.688 9.951 32.847 -3.088 -1.038 4.241 N3 DPY 10 DPY C4 C4 C 0 1 Y N N 24.717 9.124 33.188 -2.329 -1.151 5.354 C4 DPY 11 DPY C8 C8 C 0 1 N N N 24.352 8.777 34.536 -3.043 -1.055 6.615 C8 DPY 12 DPY O81 O81 O 0 1 N N N 23.405 8.000 34.792 -2.530 -1.132 7.738 O81 DPY 13 DPY O82 O82 O 0 1 N N N 25.046 9.314 35.409 -4.380 -0.861 6.445 O82 DPY 14 DPY C5 C5 C 0 1 Y N N 23.954 8.542 32.155 -0.958 -1.348 5.341 C5 DPY 15 DPY C6 C6 C 0 1 Y N N 24.255 8.873 30.823 -0.324 -1.433 4.106 C6 DPY 16 DPY "C2'" C2* C 0 1 N N N 26.834 9.445 28.488 0.128 -0.067 1.088 "C2'" DPY 17 DPY "C5'" C5* C 0 1 N N N 24.471 8.473 26.219 3.141 -2.068 1.947 "C5'" DPY 18 DPY "C4'" C4* C 0 1 N N R 25.064 9.686 26.892 1.914 -1.583 1.196 "C4'" DPY 19 DPY "O4'" O4* O 0 1 N N N 24.560 9.692 28.246 0.754 -2.299 1.648 "O4'" DPY 20 DPY "C1'" C1* C 0 1 N N R 25.617 10.114 29.081 -0.384 -1.414 1.591 "C1'" DPY 21 DPY "C3'" C3* C 0 1 N N S 26.600 9.689 27.001 1.601 -0.115 1.426 "C3'" DPY 22 DPY "O3'" O3* O 0 1 N N N 27.089 11.023 26.744 2.350 0.734 0.582 "O3'" DPY 23 DPY O3P O3P O 0 1 N Y N ? ? ? 5.842 -3.292 1.923 O3P DPY 24 DPY HOP2 2HOP H 0 0 N N N 27.059 7.287 25.864 5.025 -4.307 4.568 HOP2 DPY 25 DPY H72 H72 H 0 1 N N N 28.252 12.284 32.342 -5.130 -1.376 1.318 H72 DPY 26 DPY H82 H82 H 0 1 N N N 24.743 9.042 36.267 -4.871 -0.794 7.292 H82 DPY 27 DPY H5 H5 H 0 1 N N N 23.153 7.854 32.383 -0.386 -1.433 6.259 H5 DPY 28 DPY H6 H6 H 0 1 N N N 23.682 8.435 30.019 0.751 -1.586 4.064 H6 DPY 29 DPY "H2'1" 1H2* H 0 0 N N N 26.944 8.385 28.760 -0.000 0.001 0.000 "H2'1" DPY 30 DPY "H2'2" 2H2* H 0 0 N N N 27.774 9.891 28.844 -0.381 0.801 1.520 "H2'2" DPY 31 DPY "H5'1" 1H5* H 0 0 N N N 23.374 8.558 26.219 3.000 -1.936 3.021 "H5'1" DPY 32 DPY "H5'2" 2H5* H 0 0 N N N 24.840 8.414 25.184 4.023 -1.513 1.623 "H5'2" DPY 33 DPY "H4'" H4* H 0 1 N N N 24.785 10.556 26.279 2.051 -1.795 0.129 "H4'" DPY 34 DPY "H1'" H1* H 0 1 N N N 25.785 11.201 29.116 -1.110 -1.836 0.888 "H1'" DPY 35 DPY "H3'" H3* H 0 1 N N N 27.076 8.971 26.317 1.765 0.175 2.471 "H3'" DPY 36 DPY H3T H3T H 0 1 N Y N 26.356 11.624 26.688 3.266 0.418 0.615 H3T DPY 37 DPY HOP3 3HOP H 0 0 N N N 0.565 0.227 0.729 6.748 -3.598 2.142 HOP3 DPY 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 DPY P O1P DOUB N N 1 DPY P O2P SING N N 2 DPY P "O5'" SING N N 3 DPY P O3P SING N N 4 DPY O2P HOP2 SING N N 5 DPY "O5'" "C5'" SING N N 6 DPY C1 C2 DOUB Y N 7 DPY C1 C6 SING Y N 8 DPY C1 "C1'" SING N N 9 DPY C2 C7 SING N N 10 DPY C2 N3 SING Y N 11 DPY C7 O71 DOUB N N 12 DPY C7 O72 SING N N 13 DPY O72 H72 SING N N 14 DPY N3 C4 DOUB Y N 15 DPY C4 C8 SING N N 16 DPY C4 C5 SING Y N 17 DPY C8 O81 DOUB N N 18 DPY C8 O82 SING N N 19 DPY O82 H82 SING N N 20 DPY C5 C6 DOUB Y N 21 DPY C5 H5 SING N N 22 DPY C6 H6 SING N N 23 DPY "C2'" "C1'" SING N N 24 DPY "C2'" "C3'" SING N N 25 DPY "C2'" "H2'1" SING N N 26 DPY "C2'" "H2'2" SING N N 27 DPY "C5'" "C4'" SING N N 28 DPY "C5'" "H5'1" SING N N 29 DPY "C5'" "H5'2" SING N N 30 DPY "C4'" "O4'" SING N N 31 DPY "C4'" "C3'" SING N N 32 DPY "C4'" "H4'" SING N N 33 DPY "O4'" "C1'" SING N N 34 DPY "C1'" "H1'" SING N N 35 DPY "C3'" "O3'" SING N N 36 DPY "C3'" "H3'" SING N N 37 DPY "O3'" H3T SING N N 38 DPY O3P HOP3 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 DPY SMILES ACDLabs 10.04 "O=P(OCC2OC(c1ccc(nc1C(=O)O)C(=O)O)CC2O)(O)O" DPY SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)c2ccc(nc2C(O)=O)C(O)=O" DPY SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)c2ccc(nc2C(O)=O)C(O)=O" DPY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(nc(c1[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)C(=O)O)C(=O)O" DPY SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(nc(c1C2CC(C(O2)COP(=O)(O)O)O)C(=O)O)C(=O)O" DPY InChI InChI 1.03 "InChI=1S/C12H14NO10P/c14-7-3-8(23-9(7)4-22-24(19,20)21)5-1-2-6(11(15)16)13-10(5)12(17)18/h1-2,7-9,14H,3-4H2,(H,15,16)(H,17,18)(H2,19,20,21)/t7-,8+,9+/m0/s1" DPY InChIKey InChI 1.03 CHBIMKWOMAYTSS-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 DPY "SYSTEMATIC NAME" ACDLabs 10.04 "(1R)-1,4-anhydro-2-deoxy-1-(2,6-dicarboxypyridin-3-yl)-5-O-phosphono-D-erythro-pentitol" DPY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "3-[(2R,4S,5R)-4-hydroxy-5-(phosphonooxymethyl)oxolan-2-yl]pyridine-2,6-dicarboxylic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DPY "Create component" 2001-06-25 RCSB DPY "Modify descriptor" 2011-06-04 RCSB #