data_RED
#
_chem_comp.id RED
_chem_comp.name 'DIHYDROLIPOIC ACID'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C8 H16 O2 S2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-01-11
_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 208.341
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RED
_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 1DXM
_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
RED C1 C1 C 0 1 N N N N N N 21.478 -9.114 8.858 0.295 0.033 4.852 C1 RED 1
RED O1 O1 O 0 1 N N N N N N 21.617 -7.979 8.386 1.349 0.619 4.787 O1 RED 2
RED OXT OXT O 0 1 N Y N N N N 20.479 -9.936 8.469 -0.250 -0.236 6.049 OXT RED 3
RED C2 C2 C 0 1 N N N N N N 22.474 -9.606 9.894 -0.408 -0.394 3.590 C2 RED 4
RED C3 C3 C 0 1 N N N N N N 23.900 -9.132 9.592 0.418 0.031 2.376 C3 RED 5
RED C4 C4 C 0 1 N N N N N N 24.528 -9.920 8.440 -0.295 -0.403 1.094 C4 RED 6
RED C5 C5 C 0 1 N N N N N N 25.976 -9.511 8.185 0.531 0.023 -0.119 C5 RED 7
RED C6 C6 C 0 1 N N R N N N 26.824 -10.595 7.508 -0.182 -0.411 -1.401 C6 RED 8
RED C7 C7 C 0 1 N N N N N N 26.839 -11.876 8.346 0.644 0.015 -2.615 C7 RED 9
RED C8 C8 C 0 1 N N N N N N 27.801 -12.926 7.822 -0.069 -0.419 -3.897 C8 RED 10
RED S8 S8 S 0 1 N N N N N N 27.652 -14.529 8.619 0.911 0.085 -5.337 S8 RED 11
RED S6 S6 S 0 1 N N N N N N 28.467 -10.071 7.012 -1.816 0.372 -1.477 S6 RED 12
RED HO HO H 0 1 N N N N N N 20.372 -10.807 8.831 0.201 0.038 6.859 HO RED 13
RED H22 2H2 H 0 1 N N N N N N 22.161 -9.316 10.924 -0.524 -1.478 3.588 H22 RED 14
RED H21 1H2 H 0 1 N N N N N N 22.430 -10.715 10.001 -1.390 0.075 3.544 H21 RED 15
RED H32 2H3 H 0 1 N N N N N N 23.930 -8.034 9.397 0.534 1.115 2.377 H32 RED 16
RED H31 1H3 H 0 1 N N N N N N 24.540 -9.165 10.503 1.400 -0.439 2.422 H31 RED 17
RED H42 2H4 H 0 1 N N N N N N 24.442 -11.018 8.609 -0.411 -1.486 1.093 H42 RED 18
RED H41 1H4 H 0 1 N N N N N N 23.915 -9.835 7.512 -1.277 0.067 1.048 H41 RED 19
RED H52 2H5 H 0 1 N N N N N N 26.016 -8.561 7.601 0.647 1.107 -0.118 H52 RED 20
RED H51 1H5 H 0 1 N N N N N N 26.458 -9.172 9.131 1.513 -0.447 -0.073 H51 RED 21
RED H6 H6 H 0 1 N N N N N N 26.317 -10.815 6.539 -0.298 -1.495 -1.403 H6 RED 22
RED H72 2H7 H 0 1 N N N N N N 27.048 -11.646 9.416 0.760 1.098 -2.614 H72 RED 23
RED H71 1H7 H 0 1 N N N N N N 25.810 -12.295 8.445 1.626 -0.455 -2.569 H71 RED 24
RED H82 2H8 H 0 1 N N N N N N 27.699 -13.029 6.716 -0.185 -1.503 -3.898 H82 RED 25
RED H81 1H8 H 0 1 N N N N N N 28.851 -12.556 7.883 -1.051 0.051 -3.943 H81 RED 26
RED H8S H8S H 0 1 N N N N N N 28.254 -15.186 8.290 0.128 -0.378 -6.327 H8S RED 27
RED H6S H6S H 0 1 N N N N N N 28.992 -10.742 6.592 -1.455 1.667 -1.465 H6S RED 28
#
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
RED C1 O1 DOUB N N 1
RED C1 OXT SING N N 2
RED C1 C2 SING N N 3
RED OXT HO SING N N 4
RED C2 C3 SING N N 5
RED C2 H22 SING N N 6
RED C2 H21 SING N N 7
RED C3 C4 SING N N 8
RED C3 H32 SING N N 9
RED C3 H31 SING N N 10
RED C4 C5 SING N N 11
RED C4 H42 SING N N 12
RED C4 H41 SING N N 13
RED C5 C6 SING N N 14
RED C5 H52 SING N N 15
RED C5 H51 SING N N 16
RED C6 C7 SING N N 17
RED C6 S6 SING N N 18
RED C6 H6 SING N N 19
RED C7 C8 SING N N 20
RED C7 H72 SING N N 21
RED C7 H71 SING N N 22
RED C8 S8 SING N N 23
RED C8 H82 SING N N 24
RED C8 H81 SING N N 25
RED S8 H8S SING N N 26
RED S6 H6S SING N N 27
#
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
RED SMILES ACDLabs 10.04 'O=C(O)CCCCC(S)CCS'
RED SMILES_CANONICAL CACTVS 3.341 'OC(=O)CCCC[C@@H](S)CCS'
RED SMILES CACTVS 3.341 'OC(=O)CCCC[CH](S)CCS'
RED SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C(CCC(=O)O)C[C@H](CCS)S'
RED SMILES 'OpenEye OEToolkits' 1.5.0 'C(CCC(=O)O)CC(CCS)S'
RED InChI InChI 1.03 'InChI=1S/C8H16O2S2/c9-8(10)4-2-1-3-7(12)5-6-11/h7,11-12H,1-6H2,(H,9,10)/t7-/m1/s1'
RED InChIKey InChI 1.03 IZFHEQBZOYJLPK-SSDOTTSWSA-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
RED 'SYSTEMATIC NAME' ACDLabs 10.04 '(6R)-6,8-disulfanyloctanoic acid'
RED 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(6R)-6,8-bis-sulfanyloctanoic 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
RED 'Create component' 2000-01-11 EBI
RED 'Modify descriptor' 2011-06-04 RCSB
RED 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id RED
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type Lipoylation
_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 C1
_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 PTM-0383
_pdbx_chem_comp_pcm.first_instance_model_db_code 1DXM
#
_pdbe_chem_comp_drugbank_details.comp_id RED
_pdbe_chem_comp_drugbank_details.drugbank_id DB03760
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Dihydrolipoic Acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 462-20-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id RED
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03760
_pdbe_chem_comp_drugbank_classification.parent 'Medium-chain fatty acids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Fatty Acyls'
_pdbe_chem_comp_drugbank_classification.superclass 'Lipids and lipid-like molecules'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
RED DB03760 'Glycine cleavage system H protein, mitochondrial' Humans P23434 unknown 1
RED DB03760 'Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial' Humans P10515 unknown 2
RED DB03760 '[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial' Humans Q15120 unknown 3
RED DB03760 Aminomethyltransferase 'Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)' Q9WY54 unknown 4
#
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
RED C1 C 14.198 0.608 1
RED O1 O 15.497 -0.142 2
RED OXT O 14.198 2.107 3
RED C2 C 12.899 -0.142 4
RED C3 C 11.600 0.608 5
RED C4 C 10.301 -0.142 6
RED C5 C 9.002 0.608 7
RED C6 C 7.702 -0.142 8
RED C7 C 6.404 0.608 9
RED C8 C 5.104 -0.142 10
RED S8 S 3.805 0.608 11
RED S6 S 7.702 -1.643 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
RED C1 O1 DOUBLE NONE 1
RED C1 OXT SINGLE NONE 2
RED C1 C2 SINGLE NONE 3
RED C2 C3 SINGLE NONE 4
RED C3 C4 SINGLE NONE 5
RED C4 C5 SINGLE NONE 6
RED C5 C6 SINGLE NONE 7
RED C6 C7 SINGLE NONE 8
RED C6 S6 SINGLE BEGINWEDGE 9
RED C7 C8 SINGLE NONE 10
RED C8 S8 SINGLE NONE 11
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id RED
_pdbe_chem_comp_rdkit_properties.exactmw 208.059
_pdbe_chem_comp_rdkit_properties.amw 208.348
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 106.488
_pdbe_chem_comp_rdkit_properties.tpsa 37.300
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.250
_pdbe_chem_comp_rdkit_properties.CrippenMR 57.348
_pdbe_chem_comp_rdkit_properties.chi0v 7.266
_pdbe_chem_comp_rdkit_properties.chi1v 3.383
_pdbe_chem_comp_rdkit_properties.chi2v 0.874
_pdbe_chem_comp_rdkit_properties.chi3v 0.874
_pdbe_chem_comp_rdkit_properties.chi4v 0.517
_pdbe_chem_comp_rdkit_properties.chi0n 21.633
_pdbe_chem_comp_rdkit_properties.chi1n 10.291
_pdbe_chem_comp_rdkit_properties.chi2n 0.568
_pdbe_chem_comp_rdkit_properties.chi3n 0.568
_pdbe_chem_comp_rdkit_properties.chi4n 0.248
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.170
_pdbe_chem_comp_rdkit_properties.kappa1 2.057
_pdbe_chem_comp_rdkit_properties.kappa2 7.800
_pdbe_chem_comp_rdkit_properties.kappa3 8.268
_pdbe_chem_comp_rdkit_properties.Phi 1.337
#
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
RED UniChem ChEMBL CHEMBL1235647
RED UniChem DrugBank DB03760
RED UniChem PDBe RED
RED UniChem ChEBI 45230
RED UniChem ZINC ZINC000003869601
RED UniChem eMolecules 31430346
RED UniChem fdasrs 00K1YL9Q69
RED UniChem MetaboLights MTBLC45230
RED UniChem BRENDA 132269
RED UniChem ChemicalBook CB8855523
RED UniChem 'Probes And Drugs' PD007261
RED UniChem Nikkaji J67.184C
RED UniChem SureChEMBL SCHEMBL867951
RED UniChem 'PubChem TPHARMA' 14794355
RED UniChem PubChem 9834298
#
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
RED C1 -4.449 -0.029 -0.201 ETKDGv3 1
RED O1 -5.016 0.659 0.689 ETKDGv3 2
RED OXT -5.075 -1.163 -0.709 ETKDGv3 3
RED C2 -3.082 0.344 -0.680 ETKDGv3 4
RED C3 -2.010 -0.355 0.161 ETKDGv3 5
RED C4 -0.602 0.013 -0.322 ETKDGv3 6
RED C5 0.472 -0.682 0.534 ETKDGv3 7
RED C6 1.919 -0.441 0.052 ETKDGv3 8
RED C7 2.291 1.058 0.046 ETKDGv3 9
RED C8 3.799 1.312 -0.089 ETKDGv3 10
RED S8 4.695 0.885 1.440 ETKDGv3 11
RED S6 2.191 -1.185 -1.598 ETKDGv3 12
RED HO -5.994 -1.438 -0.384 ETKDGv3 13
RED H22 -2.955 1.447 -0.614 ETKDGv3 14
RED H21 -2.978 0.046 -1.746 ETKDGv3 15
RED H32 -2.124 -0.054 1.226 ETKDGv3 16
RED H31 -2.148 -1.457 0.089 ETKDGv3 17
RED H42 -0.495 -0.291 -1.386 ETKDGv3 18
RED H41 -0.479 1.115 -0.254 ETKDGv3 19
RED H52 0.281 -1.777 0.543 ETKDGv3 20
RED H51 0.381 -0.328 1.585 ETKDGv3 21
RED H6 2.582 -0.972 0.767 ETKDGv3 22
RED H72 1.933 1.541 0.982 ETKDGv3 23
RED H71 1.780 1.559 -0.804 ETKDGv3 24
RED H82 4.226 0.754 -0.949 ETKDGv3 25
RED H81 3.958 2.395 -0.279 ETKDGv3 26
RED H8S 4.891 -0.455 1.054 ETKDGv3 27
RED H6S 2.009 -2.499 -1.128 ETKDGv3 28
#