data_KDO
# 
_chem_comp.id                                    KDO 
_chem_comp.name                                  "3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid" 
_chem_comp.type                                  "D-saccharide, alpha linking" 
_chem_comp.pdbx_type                             ATOMS 
_chem_comp.formula                               "C8 H14 O8" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "3-deoxy-d-manno-oct-2-ulopyranosonic acid; 2-keto-3-deoxy-D-mannooctanoic acid; 3-deoxy-alpha-D-manno-oct-2-ulosonic acid; 3-deoxy-D-manno-oct-2-ulosonic acid; 3-deoxy-manno-oct-2-ulosonic acid" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_chem_comp.pdbx_modified_date                    2026-01-20 
_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                        238.192 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     KDO 
_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        1FCP 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_chem_comp.pdbx_pcm                              Y 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 KDO "3-deoxy-d-manno-oct-2-ulopyranosonic acid" PDB ? 
2 KDO "2-keto-3-deoxy-D-mannooctanoic acid"       PDB ? 
3 KDO "3-deoxy-alpha-D-manno-oct-2-ulosonic acid" PDB ? 
4 KDO "3-deoxy-D-manno-oct-2-ulosonic acid"       PDB ? 
5 KDO "3-deoxy-manno-oct-2-ulosonic acid"         PDB ? 
# 
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 
KDO C1   C1  C 0 1 N N N N N N 54.860 65.598 52.980 1.541  -0.269 -2.261 C1   KDO 1  
KDO O1A  O1A O 0 1 N N N N N N 55.576 65.023 52.137 2.364  -1.061 -1.868 O1A  KDO 2  
KDO O1B  O1B O 0 1 N N N N N N 53.631 65.746 52.830 1.565  0.146  -3.537 O1B  KDO 3  
KDO C2   C2  C 0 1 N N R N N N 55.510 66.151 54.235 0.486  0.251  -1.319 C2   KDO 4  
KDO O2   O2  O 0 1 N Y N N N N 55.212 67.494 54.366 0.602  1.671  -1.215 O2   KDO 5  
KDO C3   C3  C 0 1 N N N N N N 54.984 65.382 55.453 -0.899 -0.108 -1.859 C3   KDO 6  
KDO C4   C4  C 0 1 N N R N N N 55.773 65.751 56.715 -1.965 0.453  -0.913 C4   KDO 7  
KDO O4   O4  O 0 1 N N N N N N 55.299 64.977 57.839 -3.257 0.001  -1.323 O4   KDO 8  
KDO C5   C5  C 0 1 N N R N N N 57.265 65.480 56.463 -1.669 -0.043 0.506  C5   KDO 9  
KDO O5   O5  O 0 1 N N N N N N 57.460 64.078 56.108 -1.845 -1.460 0.563  O5   KDO 10 
KDO C6   C6  C 0 1 N N R N N N 57.657 66.392 55.298 -0.226 0.312  0.868  C6   KDO 11 
KDO O6   O6  O 0 1 N N N N N N 56.935 65.999 54.102 0.670  -0.335 -0.032 O6   KDO 12 
KDO C7   C7  C 0 1 N N R N N N 59.159 66.381 55.058 0.068  -0.147 2.297  C7   KDO 13 
KDO O7   O7  O 0 1 N N N N N N 59.791 67.072 56.121 -0.827 0.502  3.201  O7   KDO 14 
KDO C8   C8  C 0 1 N N N N N N 59.519 67.048 53.727 1.510  0.210  2.662  C8   KDO 15 
KDO O8   O8  O 0 1 N N N N N N 59.358 68.451 53.841 1.785  -0.219 3.997  O8   KDO 16 
KDO HO1B H1B H 0 0 N N N N N N 53.085 66.184 53.472 2.242  -0.187 -4.142 HO1B KDO 17 
KDO HO2  HO2 H 0 1 N Y N N N N 55.618 67.840 55.151 1.489  1.856  -0.876 HO2  KDO 18 
KDO H31  H31 H 0 1 N N N N N N 53.888 65.532 55.593 -1.027 0.325  -2.851 H31  KDO 19 
KDO H32  H32 H 0 1 N N N N N N 54.981 64.281 55.275 -0.997 -1.192 -1.918 H32  KDO 20 
KDO H4   H4  H 0 1 N N N N N N 55.628 66.830 56.951 -1.936 1.543  -0.933 H4   KDO 21 
KDO HO4  HO4 H 0 1 N Y N N N N 55.787 65.205 58.620 -3.394 0.325  -2.223 HO4  KDO 22 
KDO H5   H5  H 0 1 N N N N N N 57.888 65.682 57.365 -2.349 0.437  1.210  H5   KDO 23 
KDO HO5  HO5 H 0 1 N Y N N N N 58.382 63.910 55.952 -2.765 -1.637 0.323  HO5  KDO 24 
KDO H6   H6  H 0 1 N N N N N N 57.377 67.438 55.562 -0.091 1.392  0.800  H6   KDO 25 
KDO H7   H7  H 0 1 N N N N N N 59.507 65.322 55.013 -0.066 -1.227 2.366  H7   KDO 26 
KDO HO7  HO7 H 0 1 N Y N N N N 60.729 67.065 55.971 -0.676 1.453  3.109  HO7  KDO 27 
KDO H81  H81 H 0 1 N N N N N N 60.540 66.768 53.378 1.645  1.289  2.593  H81  KDO 28 
KDO H82  H82 H 0 1 N N N N N N 58.938 66.625 52.873 2.193  -0.285 1.973  H82  KDO 29 
KDO HO8  HO8 H 0 1 N Y N N N N 59.581 68.864 53.015 2.701  0.024  4.186  HO8  KDO 30 
# 
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 
KDO C1  O1A  DOUB N N 1  
KDO C1  O1B  SING N N 2  
KDO C1  C2   SING N N 3  
KDO O1B HO1B SING N N 4  
KDO C2  O2   SING N N 5  
KDO C2  C3   SING N N 6  
KDO C2  O6   SING N N 7  
KDO O2  HO2  SING N N 8  
KDO C3  C4   SING N N 9  
KDO C3  H31  SING N N 10 
KDO C3  H32  SING N N 11 
KDO C4  O4   SING N N 12 
KDO C4  C5   SING N N 13 
KDO C4  H4   SING N N 14 
KDO O4  HO4  SING N N 15 
KDO C5  O5   SING N N 16 
KDO C5  C6   SING N N 17 
KDO C5  H5   SING N N 18 
KDO O5  HO5  SING N N 19 
KDO C6  O6   SING N N 20 
KDO C6  C7   SING N N 21 
KDO C6  H6   SING N N 22 
KDO C7  O7   SING N N 23 
KDO C7  C8   SING N N 24 
KDO C7  H7   SING N N 25 
KDO O7  HO7  SING N N 26 
KDO C8  O8   SING N N 27 
KDO C8  H81  SING N N 28 
KDO C8  H82  SING N N 29 
KDO O8  HO8  SING N N 30 
# 
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 
KDO SMILES           ACDLabs              10.04 "O=C(O)C1(O)OC(C(O)CO)C(O)C(O)C1"                                                                                
KDO SMILES_CANONICAL CACTVS               3.341 "OC[C@@H](O)[C@H]1O[C@](O)(C[C@@H](O)[C@H]1O)C(O)=O"                                                             
KDO SMILES           CACTVS               3.341 "OC[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O"                                                                    
KDO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@H]([C@H](O[C@]1(C(=O)O)O)[C@@H](CO)O)O)O"                                                            
KDO SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(C(OC1(C(=O)O)O)C(CO)O)O)O"                                                                                
KDO InChI            InChI                1.03  "InChI=1S/C8H14O8/c9-2-4(11)6-5(12)3(10)1-8(15,16-6)7(13)14/h3-6,9-12,15H,1-2H2,(H,13,14)/t3-,4-,5-,6-,8-/m1/s1" 
KDO InChIKey         InChI                1.03  NNLZBVFSCVTSLA-HXUQBWEZSA-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 
KDO "SYSTEMATIC NAME"                     ACDLabs              10.04 "3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid"                                    
KDO "SYSTEMATIC NAME"                     "OpenEye OEToolkits" 1.5.0 "(2R,4R,5R,6R)-6-[(1R)-1,2-dihydroxyethyl]-2,4,5-trihydroxy-oxane-2-carboxylic acid" 
KDO "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML                 1.0   DKdopa                                                                               
KDO "IUPAC CARBOHYDRATE SYMBOL"           PDB-CARE             1.0   a-D-Kdop                                                                             
KDO "SNFG CARBOHYDRATE SYMBOL"            GMML                 1.0   Kdo                                                                                  
# 
loop_
_pdbx_chem_comp_feature.comp_id 
_pdbx_chem_comp_feature.type 
_pdbx_chem_comp_feature.value 
_pdbx_chem_comp_feature.source 
_pdbx_chem_comp_feature.support 
KDO "CARBOHYDRATE ISOMER"                 D        PDB ? 
KDO "CARBOHYDRATE RING"                   pyranose PDB ? 
KDO "CARBOHYDRATE ANOMER"                 alpha    PDB ? 
KDO "CARBOHYDRATE PRIMARY CARBONYL GROUP" ketose   PDB ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
KDO "Create component"         1999-07-08 EBI  
KDO "Modify descriptor"        2011-06-04 RCSB 
KDO "Other modification"       2019-08-12 RCSB 
KDO "Other modification"       2019-12-19 RCSB 
KDO "Other modification"       2020-07-03 RCSB 
KDO "Modify name"              2020-07-17 RCSB 
KDO "Modify synonyms"          2020-07-17 RCSB 
KDO "Modify atom id"           2020-07-17 RCSB 
KDO "Modify component atom id" 2020-07-17 RCSB 
KDO "Modify PCM"               2026-01-20 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            KDO 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_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               C2 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
