Database accession: MF7000463
Name: Human Glyoxalase I with N-hydroxypyridone inhibitor
PDB ID: 3vw9
Experimental method: X-ray (1.47 Å)
Assembly: Homodimer
Source organism: Homo sapiens
Primary publication of the structure:
Chiba T, Ohwada J, Sakamoto H, Kobayashi T, Fukami TA, Irie M, Miura T, Ohara K, Koyano H
Design and evaluation of azaindole-substituted N-hydroxypyridones as glyoxalase I inhibitors.
(2012) Bioorg. Med. Chem. Lett. 22: 7486-9
PMID: 23122816
Abstract:
We conducted a high throughput screening for glyoxalase I (GLO1) inhibitors and identified 4,6-diphenyl-N-hydroxypyridone as a lead compound. Using a binding model of the lead and public X-ray coordinates of GLO1 enzymes complexed with glutathione analogues, we designed 4-(7-azaindole)-substituted 6-phenyl-N-hydroxypyridones. 7-Azaindole's 7-nitrogen was expected to interact with a water network, resulting in an interaction with the protein. We validated this inhibitor design by comparing its structure-activity relationship (SAR) with that of corresponding indole derivatives, by analyzing the binding mode with X-ray crystallography and by evaluating its thermodynamic binding parameters.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
lactoylglutathione lyase activity lactoylglutathione lyase activity
zinc ion binding zinc ion binding
Biological process:
carbohydrate metabolic process carbohydrate metabolic process
glutathione metabolic process glutathione metabolic process
methylglyoxal metabolic process methylglyoxal metabolic process
negative regulation of apoptotic process negative regulation of apoptotic process
osteoclast differentiation osteoclast differentiation
regulation of transcription by RNA polymerase II regulation of transcription by RNA polymerase II
Cellular component:
cytoplasm cytoplasm
cytosol cytosol
extracellular exosome extracellular exosome
nucleoplasm nucleoplasm
plasma membrane plasma membrane
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Lactoylglutathione lyase
Source organism: Homo sapiens
Length: 184 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAEPQPPSGGLTDEAALSCCSDADPSTKDFLLQQTMLRVKDPKKSLDFYTRVLGMTLIQKCDFPIMKFSLYFLAYEDKNDIPKEKDEKIAWALSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKMATLM
UniProtKB AC: Q04760 (positions: 9-184)
Coverage: 95%
Name: Lactoylglutathione lyase
Source organism: Homo sapiens
Length: 184 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAEPQPPSGGLTDEAALSCCSDADPSTKDFLLQQTMLRVKDPKKSLDFYTRVLGMTLIQKCDFPIMKFSLYFLAYEDKNDIPKEKDEKIAWALSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKMATLM
UniProtKB AC: Q04760 (positions: 9-184)
Coverage: 95%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The VOC superfamily of metalloenzymes is characterized by a three-dimensional domain-swapped arrangement of tandem βαβββ-motifs (PMID:24447055). The original gene duplication event led to the βαβββ tandem structure, which appears to require dimerization for stability. Two different forms of domain-swapped dimers may coexist in solution (PMID:12121648) in which both subunits of the homodimer participate in coordination of each metal ion and formation of the U-shaped active sites in the enzyme (PMID:24004181). The complex is predominantly dimeric in solution (gel filtration) (PMID:12121648).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
