data_SSH
#
_chem_comp.id SSH
_chem_comp.name '3-DEOXY-D-ARABINO-HEXONIC ACID'
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula 'C6 H12 O6'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms D-2-KETO-3-DEOXYGLUCONATE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-07-17
_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 180.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SSH
_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 1W3N
_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
SSH O2 O2 O 0 1 N N N N N N -14.098 62.103 12.584 -3.214 0.701 -1.413 O2 SSH 1
SSH C1 C1 C 0 1 N N N N N N -14.338 62.750 13.663 -2.948 0.005 -0.296 C1 SSH 2
SSH O1 O1 O 0 1 N N N N N N -14.653 63.975 13.704 -3.716 -0.848 0.081 O1 SSH 3
SSH C2 C2 C 0 1 N N S N N N -14.230 62.118 15.008 -1.691 0.287 0.486 C2 SSH 4
SSH C3 C3 C 0 1 N N N N N N -13.610 60.720 15.079 -0.470 -0.078 -0.361 C3 SSH 5
SSH C4 C4 C 0 1 N N S N N N -12.044 60.932 15.200 0.805 0.324 0.383 C4 SSH 6
SSH O4 O4 O 0 1 N N N N N N -11.805 62.352 15.230 0.850 1.746 0.518 O4 SSH 7
SSH C5 C5 C 0 1 N N R N N N -11.308 60.334 13.984 2.027 -0.152 -0.405 C5 SSH 8
SSH O5 O5 O 0 1 N N N N N N -11.812 58.995 13.840 1.982 -1.574 -0.540 O5 SSH 9
SSH C6 C6 C 0 1 N N N N N N -9.785 60.152 14.164 3.302 0.249 0.339 C6 SSH 10
SSH O6 O6 O 0 1 N N N N N N -9.289 59.854 12.848 4.442 -0.091 -0.452 O6 SSH 11
SSH OT OT O 0 1 N Y N N N N -15.235 62.102 15.491 -1.690 -0.493 1.684 OT SSH 12
SSH H2 H2 H 0 1 N N N N N N -14.194 62.684 11.838 -4.020 0.520 -1.915 H2 SSH 13
SSH H2C1 1H2C H 0 0 N N N N N N -13.510 62.755 15.543 -1.652 1.346 0.742 H2C1 SSH 14
SSH H3C1 1H3C H 0 0 N N N N N N -13.863 60.127 14.188 -0.517 0.451 -1.313 H3C1 SSH 15
SSH H3C2 2H3C H 0 0 N N N N N N -13.994 60.172 15.952 -0.462 -1.153 -0.542 H3C2 SSH 16
SSH H4 H4 H 0 1 N N N N N N -11.673 60.433 16.107 0.809 -0.135 1.372 H4 SSH 17
SSH HA HA H 0 1 N N N N N N -11.752 62.646 16.132 0.845 2.112 -0.377 HA SSH 18
SSH H5 H5 H 0 1 N N N N N N -11.473 61.024 13.144 2.023 0.307 -1.394 H5 SSH 19
SSH HB HB H 0 1 N N N N N N -11.923 58.795 12.918 1.987 -1.940 0.355 HB SSH 20
SSH H6C1 1H6C H 0 0 N N N N N N -9.548 59.355 14.884 3.349 -0.279 1.291 H6C1 SSH 21
SSH H6C2 2H6C H 0 0 N N N N N N -9.323 61.068 14.562 3.294 1.324 0.520 H6C2 SSH 22
SSH H6 H6 H 0 1 N N N N N N -10.018 59.788 12.242 5.222 0.178 0.052 H6 SSH 23
SSH HT HT H 0 1 N N N N N N -15.133 62.097 16.435 -1.725 -1.421 1.413 HT SSH 24
#
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
SSH O2 C1 SING N N 1
SSH O2 H2 SING N N 2
SSH C1 O1 DOUB N N 3
SSH C1 C2 SING N N 4
SSH C2 C3 SING N N 5
SSH C2 OT SING N N 6
SSH C2 H2C1 SING N N 7
SSH C3 C4 SING N N 8
SSH C3 H3C1 SING N N 9
SSH C3 H3C2 SING N N 10
SSH C4 O4 SING N N 11
SSH C4 C5 SING N N 12
SSH C4 H4 SING N N 13
SSH O4 HA SING N N 14
SSH C5 O5 SING N N 15
SSH C5 C6 SING N N 16
SSH C5 H5 SING N N 17
SSH O5 HB SING N N 18
SSH C6 O6 SING N N 19
SSH C6 H6C1 SING N N 20
SSH C6 H6C2 SING N N 21
SSH O6 H6 SING N N 22
SSH OT HT SING N N 23
#
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
SSH SMILES ACDLabs 10.04 'O=C(O)C(O)CC(O)C(O)CO'
SSH SMILES_CANONICAL CACTVS 3.341 'OC[C@@H](O)[C@@H](O)C[C@H](O)C(O)=O'
SSH SMILES CACTVS 3.341 'OC[CH](O)[CH](O)C[CH](O)C(O)=O'
SSH SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C([C@@H]([C@@H](CO)O)O)[C@@H](C(=O)O)O'
SSH SMILES 'OpenEye OEToolkits' 1.5.0 'C(C(C(CO)O)O)C(C(=O)O)O'
SSH InChI InChI 1.03 'InChI=1S/C6H12O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3-5,7-10H,1-2H2,(H,11,12)/t3-,4-,5+/m0/s1'
SSH InChIKey InChI 1.03 YGMNHEPVTNXLLS-VAYJURFESA-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
SSH 'SYSTEMATIC NAME' ACDLabs 10.04 '3-deoxy-D-arabino-hexonic acid'
SSH 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S,4S,5R)-2,4,5,6-tetrahydroxyhexanoic 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
SSH 'Create component' 2004-07-17 EBI
SSH 'Modify descriptor' 2011-06-04 RCSB
SSH 'Modify linking type' 2020-06-24 RCSB
SSH 'Modify synonyms' 2021-03-01 PDBE
SSH 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SSH
_pdbx_chem_comp_synonyms.name D-2-KETO-3-DEOXYGLUCONATE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id SSH
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category Carbohydrate
_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 NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 1W3N
#
_pdbe_chem_comp_drugbank_details.comp_id SSH
_pdbe_chem_comp_drugbank_details.drugbank_id DB03303
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '3-deoxy-D-arabino-hexonic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 29625-79-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
SSH D-2-KETO-3-DEOXYGLUCONATE wwPDB ?
SSH '3-Deoxy-arabino-hexonic acid' DrugBank ?
SSH D-2-keto-3-deoxygluconate DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id SSH
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03303
_pdbe_chem_comp_drugbank_classification.parent 'Medium-chain hydroxy acids and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Hydroxy acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.'
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
SSH O2 O 3.805 -0.375 1
SSH C1 C 5.104 0.375 2
SSH O1 O 5.104 1.875 3
SSH C2 C 6.404 -0.375 4
SSH C3 C 7.702 0.375 5
SSH C4 C 9.002 -0.375 6
SSH O4 O 9.002 -1.875 7
SSH C5 C 10.301 0.375 8
SSH O5 O 10.301 1.875 9
SSH C6 C 11.600 -0.375 10
SSH O6 O 12.899 0.375 11
SSH OT O 6.404 -1.875 12
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
SSH O2 C1 SINGLE NONE 1
SSH C1 O1 DOUBLE NONE 2
SSH C1 C2 SINGLE NONE 3
SSH C2 C3 SINGLE NONE 4
SSH C2 OT SINGLE BEGINDASH 5
SSH C3 C4 SINGLE NONE 6
SSH C4 O4 SINGLE BEGINWEDGE 7
SSH C4 C5 SINGLE NONE 8
SSH C5 O5 SINGLE BEGINDASH 9
SSH C5 C6 SINGLE NONE 10
SSH C6 O6 SINGLE NONE 11
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id SSH
_pdbe_chem_comp_rdkit_properties.exactmw 180.063
_pdbe_chem_comp_rdkit_properties.amw 180.156
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 85.990
_pdbe_chem_comp_rdkit_properties.tpsa 118.220
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.464
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.359
_pdbe_chem_comp_rdkit_properties.chi0v 5.449
_pdbe_chem_comp_rdkit_properties.chi1v 2.475
_pdbe_chem_comp_rdkit_properties.chi2v 0.711
_pdbe_chem_comp_rdkit_properties.chi3v 0.711
_pdbe_chem_comp_rdkit_properties.chi4v 0.257
_pdbe_chem_comp_rdkit_properties.chi0n 17.449
_pdbe_chem_comp_rdkit_properties.chi1n 8.016
_pdbe_chem_comp_rdkit_properties.chi2n 0.711
_pdbe_chem_comp_rdkit_properties.chi3n 0.711
_pdbe_chem_comp_rdkit_properties.chi4n 0.257
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.690
_pdbe_chem_comp_rdkit_properties.kappa1 2.415
_pdbe_chem_comp_rdkit_properties.kappa2 5.044
_pdbe_chem_comp_rdkit_properties.kappa3 3.629
_pdbe_chem_comp_rdkit_properties.Phi 1.015
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
SSH UniChem DrugBank DB03303
SSH UniChem PDBe SSH
SSH UniChem ChEBI 45626
SSH UniChem ZINC ZINC000004803503
SSH UniChem HMDB HMDB0000346
SSH UniChem ACTor 29625-79-4
SSH UniChem Nikkaji J14.953E
SSH UniChem MetaboLights MTBLC45626
SSH UniChem 'Probes And Drugs' PD059695
SSH UniChem PubChem 152990
SSH UniChem SureChEMBL SCHEMBL3776284
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
SSH O2 -3.424 1.222 -0.818 ETKDGv3 1
SSH C1 -3.060 0.641 0.394 ETKDGv3 2
SSH O1 -3.598 1.032 1.464 ETKDGv3 3
SSH C2 -1.997 -0.419 0.430 ETKDGv3 4
SSH C3 -0.609 0.232 0.299 ETKDGv3 5
SSH C4 0.538 -0.804 0.400 ETKDGv3 6
SSH O4 0.461 -1.517 1.611 ETKDGv3 7
SSH C5 1.946 -0.174 0.250 ETKDGv3 8
SSH O5 2.118 0.855 1.192 ETKDGv3 9
SSH C6 2.198 0.364 -1.171 ETKDGv3 10
SSH O6 3.545 0.720 -1.328 ETKDGv3 11
SSH OT -2.198 -1.324 -0.624 ETKDGv3 12
SSH H2 -4.129 1.948 -0.855 ETKDGv3 13
SSH H2C1 -2.054 -0.956 1.406 ETKDGv3 14
SSH H3C1 -0.557 0.752 -0.681 ETKDGv3 15
SSH H3C2 -0.489 0.996 1.098 ETKDGv3 16
SSH H4 0.411 -1.543 -0.421 ETKDGv3 17
SSH HA 0.532 -0.860 2.352 ETKDGv3 18
SSH H5 2.686 -0.987 0.445 ETKDGv3 19
SSH HB 3.095 0.975 1.315 ETKDGv3 20
SSH H6C1 1.580 1.269 -1.349 ETKDGv3 21
SSH H6C2 1.915 -0.397 -1.933 ETKDGv3 22
SSH H6 4.051 -0.126 -1.444 ETKDGv3 23
SSH HT -2.964 -1.900 -0.364 ETKDGv3 24
#