Structure of PDB 8pf8 Chain A Binding Site BS02

Receptor Information
>8pf8 Chain A (length=729) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSHHHHHHSMPDNTIQWDKDADGIVTLTMDDPSGSTNVMNEAYIESMGKA
VDRLVAEKDSITGVVVASAKKTFFAGGDVKTMIQARPEDAGDVFNTVETI
KRQLRTLETLGKPVVAAINGAALGGGLEIALACHHRIAADVKGSQLGLPE
VTLGLLPGGGGVTRTVRMFGIQNAFVSVLAQGTRFKPAKAKEIGLVDELV
ATVEELVPAAKAWIKEELKANPDGAGVQPWDKKGYKMPGGTPSSPGLAAI
LPSFPSNLRKQLKGAPMPAPRAILAAAVEGAQVDFDTASRIESRYFASLV
TGQVAKNMMQAFFFDLQAINAGGSRPEGIGKTPIKRIGVLGAGMMGAGIA
YVSAKAGYEVVLKDVSLEAAAKGKGYSEKLEAKALERGRTTQERSDALLA
RITPTADAADFKGVDFVIEAVFENQELKHKVFGEIEDIVEPNAILGSNTS
TLPITGLATGVKRQEDFIGIHFFSPVDKMPLVEIIKGEKTSDEALARVFD
YTLAIGKTPIVVNDSRGFFTSRVIGTFVNEALAMLGEGVEPASIEQAGSQ
AGYPAPPLQLSDELNLELMHKIAVATRKGVEDAGGTYQPHPAEAVVEKMI
ELGRSGRLKGAGFYEYADGKRSGLWPGLRETFKSGSSQPPLQDMIDRMLF
AEALETQKCLDEGVLTSTADANIGSIMGIGFPPWTGGSAQFIVGYSGPAG
TGKAAFVARARELAAAYGDRFLPPESLLS
Ligand information
Ligand IDYLZ
InChIInChI=1S/C8H12BF3N2O4/c1-14-7(2-6(13-14)8(10,11)12)9(17)18-4-5(16)3-15/h2,5,15-17H,3-4H2,1H3
InChIKeyYSSTVIJJFZPQNG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7B(c1cc(nn1C)C(F)(F)F)(O)OCC(CO)O
CACTVS 3.385Cn1nc(cc1B(O)OC[CH](O)CO)C(F)(F)F
CACTVS 3.385Cn1nc(cc1B(O)OC[C@H](O)CO)C(F)(F)F
OpenEye OEToolkits 2.0.7B(c1cc(nn1C)C(F)(F)F)(O)OC[C@@H](CO)O
FormulaC8 H12 B F3 N2 O4
Name[(2~{R})-2,3-bis(oxidanyl)propoxy]-[2-methyl-5-(trifluoromethyl)pyrazol-3-yl]borinic acid
ChEMBL
DrugBank
ZINC
PDB chain8pf8 Chain A Residue 808 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8pf8 Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate channeling path between them
Resolution2.23 Å
Binding residue
(original residue number in PDB)
M30 G68 D69 M73 V84
Binding residue
(residue number reindexed from 1)
M39 G77 D78 M82 V93
Annotation score1
Enzymatic activity
Enzyme Commision number 1.1.1.35: 3-hydroxyacyl-CoA dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity
GO:0004300 enoyl-CoA hydratase activity
GO:0016491 oxidoreductase activity
GO:0016509 long-chain-3-hydroxyacyl-CoA dehydrogenase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0016829 lyase activity
GO:0070403 NAD+ binding
Biological Process
GO:0006631 fatty acid metabolic process
GO:0006635 fatty acid beta-oxidation
GO:0009056 catabolic process
GO:0016042 lipid catabolic process
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8pf8, PDBe:8pf8, PDBj:8pf8
PDBsum8pf8
PubMed39012716
UniProtO53872

[Back to BioLiP]