data_KDG
# 
_chem_comp.id                                    KDG 
_chem_comp.name                                  2-KETO-3-DEOXYGLUCONATE 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C6 H10 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-04-12 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        178.140 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     KDG 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1V1A 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
KDG O1B  O1B  O 0 1 N N N N N N 28.286 42.767 26.389 -0.207 -0.189 4.483  O1B  KDG 1  
KDG C1   C1   C 0 1 N N N N N N 28.664 41.959 27.506 0.503  0.129  3.285  C1   KDG 2  
KDG C2   C2   C 0 1 N N R N N N 27.525 41.982 28.494 -0.369 -0.199 2.072  C2   KDG 3  
KDG O2   O2   O 0 1 N N N N N N 26.455 41.275 27.931 -1.573 0.567  2.129  O2   KDG 4  
KDG C3   C3   C 0 1 N N S N N N 27.912 41.383 29.871 0.392  0.142  0.789  C3   KDG 5  
KDG O3   O3   O 0 1 N N N N N N 29.077 42.019 30.410 1.596  -0.625 0.732  O3   KDG 6  
KDG C4   C4   C 0 1 N N N N N N 26.765 41.527 30.878 -0.480 -0.186 -0.423 C4   KDG 7  
KDG O5   O5   O 0 1 N N N N N N 26.122 43.821 30.472 1.386  0.604  -1.623 O5   KDG 8  
KDG C5   C5   C 0 1 N N N N N N 25.758 42.645 30.564 0.269  0.149  -1.687 C5   KDG 9  
KDG C6   C6   C 0 1 N N N N N N 24.289 42.293 30.342 -0.367 -0.080 -3.015 C6   KDG 10 
KDG O6A  O6A  O 0 1 N N N N N N 23.989 41.273 29.691 0.302  0.220  -4.143 O6A  KDG 11 
KDG O6B  O6B  O 0 1 N N N N N N 23.428 43.050 30.827 -1.488 -0.537 -3.079 O6B  KDG 12 
KDG H1B  H1B  H 0 1 N N N N N N 29.004 42.752 25.767 0.375  0.032  5.222  H1B  KDG 13 
KDG H1C1 1H1C H 0 0 N N N N N N 28.962 40.926 27.212 0.748  1.191  3.280  H1C1 KDG 14 
KDG H1C2 2H1C H 0 0 N N N N N N 29.635 42.270 27.957 1.421  -0.455 3.241  H1C2 KDG 15 
KDG H2   H2   H 0 1 N N N N N N 27.209 43.041 28.645 -0.614 -1.261 2.077  H2   KDG 16 
KDG HA   HA   H 0 1 N N N N N N 25.737 41.290 28.553 -1.312 1.499  2.122  HA   KDG 17 
KDG H3   H3   H 0 1 N N N N N N 28.131 40.298 29.736 0.637  1.204  0.784  H3   KDG 18 
KDG HB   HB   H 0 1 N N N N N N 29.314 41.652 31.254 1.335  -1.556 0.739  HB   KDG 19 
KDG H4C1 1H4C H 0 0 N N N N N N 27.172 41.655 31.908 -0.725 -1.248 -0.418 H4C1 KDG 20 
KDG H4C2 2H4C H 0 0 N N N N N N 26.234 40.554 30.997 -1.398 0.398  -0.380 H4C2 KDG 21 
KDG H6A  H6A  H 0 1 N N N N N N 23.075 41.054 29.552 -0.110 0.071  -5.005 H6A  KDG 22 
# 
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 
KDG O1B C1   SING N N 1  
KDG O1B H1B  SING N N 2  
KDG C1  C2   SING N N 3  
KDG C1  H1C1 SING N N 4  
KDG C1  H1C2 SING N N 5  
KDG C2  O2   SING N N 6  
KDG C2  C3   SING N N 7  
KDG C2  H2   SING N N 8  
KDG O2  HA   SING N N 9  
KDG C3  O3   SING N N 10 
KDG C3  C4   SING N N 11 
KDG C3  H3   SING N N 12 
KDG O3  HB   SING N N 13 
KDG C4  C5   SING N N 14 
KDG C4  H4C1 SING N N 15 
KDG C4  H4C2 SING N N 16 
KDG O5  C5   DOUB N N 17 
KDG C5  C6   SING N N 18 
KDG C6  O6A  SING N N 19 
KDG C6  O6B  DOUB N N 20 
KDG O6A H6A  SING N N 21 
# 
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 
KDG SMILES           ACDLabs              10.04 "O=C(C(=O)O)CC(O)C(O)CO"                                                                 
KDG SMILES_CANONICAL CACTVS               3.341 "OC[C@@H](O)[C@@H](O)CC(=O)C(O)=O"                                                       
KDG SMILES           CACTVS               3.341 "OC[CH](O)[CH](O)CC(=O)C(O)=O"                                                           
KDG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O"                                                     
KDG SMILES           "OpenEye OEToolkits" 1.5.0 "C(C(C(CO)O)O)C(=O)C(=O)O"                                                               
KDG InChI            InChI                1.03  "InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5+/m0/s1" 
KDG InChIKey         InChI                1.03  WPAMZTWLKIDIOP-WVZVXSGGSA-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 
KDG "SYSTEMATIC NAME" ACDLabs              10.04 "3-deoxy-D-erythro-hex-2-ulosonic acid"        
KDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(4S,5R)-4,5,6-trihydroxy-2-oxo-hexanoic 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 
KDG "Create component"  2004-04-12 EBI  
KDG "Modify descriptor" 2011-06-04 RCSB 
KDG "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            KDG 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           Lipid/lipid-like 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C5 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
