Human MMP13 in complex with L-glutamate motif inhibitor

Experimental Data Snapshot

  • Resolution: 2.43 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Simple pseudo-dipeptides with a P2' glutamate: a novel inhibitor family of matrix metalloproteases and other metzincins.

Devel, L.Beau, F.Amoura, M.Vera, L.Cassar-Lajeunesse, E.Garcia, S.Czarny, B.Stura, E.A.Dive, V.

(2012) J Biol Chem 287: 26647-26656

  • DOI: https://doi.org/10.1074/jbc.M112.380782
  • Primary Citation of Related Structures:  
    3TS4, 3TSK, 3TT4, 3TVC, 4EFS

  • PubMed Abstract: 

    A series of pseudo-peptides with general formula X-l-Glu-NH(2) (with X corresponding to an acyl moiety with a long aryl-alkyl side chain) have been synthesized, evaluated as inhibitors of matrix metalloproteases (MMPs), and found to display remarkable nanomolar affinity. The loss in potency associated with a substitution of the P(2)' l-glutamate by a l-glutamine corroborates the importance of a carboxylate at this position. The binding mode of some of these inhibitors was characterized in solution and by x-ray crystallography in complex with various MMPs. The x-ray crystal structures reveal an unusual binding mode with the glutamate side chain chelating the active site zinc ion. Competition experiments between these inhibitors and acetohydroxamic acid, a small zinc-binding molecule, are in accord with the crystallographic results. One of these pseudo-dipeptides displays potency and selectivity toward MMP-12 similar to the best MMP-12 inhibitors reported to date. This novel family of pseudo peptides opens new opportunities to develop potent and selective inhibitors for several metzincins.

  • Organizational Affiliation

    CEA (Commissariat à l'Energie Atomique), iBiTec-S, Service d'Ingénierie Moléculaire de Protéines (SIMOPRO), CE Saclay, 91191 Gif/Yvette, Cedex, France. laurent.devel@cea.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagenase 3169Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
PHAROS:  P45452
GTEx:  ENSG00000137745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45452
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on E3P

Download Ideal Coordinates CCD File 
G [auth A]N~2~-[3-(1,1':4',1''-terphenyl-4-yl)propanoyl]-L-alpha-glutamine
C26 H26 N2 O4
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A]
C4 H10 O3
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
E3P BindingDB:  3TVC Ki: 18 (nM) from 1 assay(s)
PDBBind:  3TVC Ki: 18 (nM) from 1 assay(s)
Binding MOAD:  3TVC Ki: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.43 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.303α = 90
b = 85.16β = 90
c = 40.916γ = 90
Software Package:
Software NamePurpose
DNAdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description