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 
# 
