Crystal structure of mouse glyoxalase I complexed with methyl-gerfelin

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


The identification of an osteoclastogenesis inhibitor through the inhibition of glyoxalase I

Kawatani, M.Okumura, H.Honda, K.Kanoh, N.Muroi, M.Dohmae, N.Takami, M.Kitagawa, M.Futamura, Y.Imoto, M.Osada, H.

(2008) Proc Natl Acad Sci U S A 105: 11691-11696

  • DOI: https://doi.org/10.1073/pnas.0712239105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Osteoclasts, bone-resorptive multinucleated cells derived from hematopoietic stem cells, are associated with many bone-related diseases, such as osteoporosis. Osteoclast-targeting small-molecule inhibitors are valuable tools for studying osteoclast biology and for developing antiresorptive agents. Here, we have discovered that methyl-gerfelin (M-GFN), the methyl ester of the natural product gerfelin, suppresses osteoclastogenesis. By using M-GFN-immobilized beads, glyoxalase I (GLO1) was identified as an M-GFN-binding protein. GLO1 knockdown and treatment with an established GLO1 inhibitor in osteoclast progenitor cells interfered with osteoclast generation, suggesting that GLO1 activity is required for osteoclastogenesis. In cells, GLO1 plays a critical role in the detoxification of 2-oxoaldehydes, such as methylglyoxal. M-GFN inhibited the enzymatic activity of GLO1 in vitro and in situ. Furthermore, the cocrystal structure of the GLO1/M-GFN complex revealed the binding mode of M-GFN at the active site of GLO1. These results suggest that M-GFN targets GLO1, resulting in the inhibition of osteoclastogenesis.

  • Organizational Affiliation

    Antibiotics Laboratory, Chemical Biology Department, and Biomolecular Characterization Team, Advanced Technology Support Division, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyoxalase I
A, B
184Mus musculusMutation(s): 0 
Gene Names: Glo1
Find proteins for Q9CPU0 (Mus musculus)
Explore Q9CPU0 
Go to UniProtKB:  Q9CPU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CPU0
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
MGI PDBBind:  2ZA0 Ki: 230 (nM) from 1 assay(s)
Binding MOAD:  2ZA0 Ki: 230 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.982α = 90
b = 65.314β = 101.18
c = 66.159γ = 90
Software Package:
Software NamePurpose
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description