Crystal Structure Analysis of human Macrophage Elastase MMP-12

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structure of human macrophage elastase (MMP-12) in complex with a hydroxamic acid inhibitor.

Nar, H.Werle, K.Bauer, M.M.Dollinger, H.Jung, B.

(2001) J Mol Biol 312: 743-751

  • DOI: https://doi.org/10.1006/jmbi.2001.4953
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human macrophage elastase (MMP-12) is a member of the family of matrix metalloproteinases (MMPs) that plays, like other members of the family, an important role in inflammatory processes contributing to tissue remodelling and destruction. In particular, a prominent role of MMP-12 in the destruction of elastin in the lung alveolar wall and the pathogenesis of emphysema has been suggested. It is therefore an attractive therapeutic target. We describe here the crystal structure of the catalytic domain of MMP-12 in complex with a hydroxamic acid inhibitor, CGS27023A. MMP-12 adopts the typical MMP fold and binds a structural zinc ion and three calcium ions in addition to the catalytic zinc ion. The enzyme structure shows an ordered N terminus close to the active site that is identical in conformation with the superactivated form of MMP-8. The S1'-specificity pocket is large and extends into a channel through the protein, which puts MMP-12 into the class of MMPs 3, 8 and 13 with large and open specificity pockets. The two crystallographically independent molecules adopt different conformations of the S1'-loop and its neighbouring loop due to differing crystal packing environments, suggesting that flexibility or the possibility of structural adjustments of these loop segments are intrinsic features of the MMP-12 structure and probably a common feature for all MMPs. The inhibitor binds in a bidentate fashion to the catalytic zinc ion. Its polar groups form hydrogen bonds in a substrate-like manner with beta-strand sIV of the enzyme, while the hydrophobic substituents are either positioned on the protein surface and are solvent-exposed or fill the upper part of the specificity pocket. The present structure enables us to aid the design of potent and selective inhibitors for MMP-12.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Boehringer Ingelheim Pharma KG, Biberach, Germany. herbert.nar@bc.boehringer-ingelheim.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
macrophage elastase MMP-12
A, B
166Homo sapiensMutation(s): 0 
Gene Names: MMP12HME
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
PHAROS:  P39900
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39900
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CGS

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
C18 H23 N3 O5 S
Query on ZN

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

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
CGS PDBBind:  1JIZ IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.4α = 90
b = 87.2β = 90
c = 169.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance