1GKD

MMP9 active site mutant-inhibitor complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal Structure of Mmp9 in Complex with a Reverse Hydroxamate Inhibitor

Rowsell, S., Hawtin, P., Minshull, C.A., Jepson, H., Brockbank, S., Barratt, D., Slater, A.M., Mcpheat, W., Waterson, D., Henney, A., Pauptit, R.A.

(2002) J Mol Biol 319: 173

  • DOI: 10.1016/S0022-2836(02)00262-0
  • Primary Citation of Related Structures:  
    1GKC, 1GKD

  • PubMed Abstract: 

    • Matrix metalloproteinases (MMPs) and their inhibitors are important in connective tissue re-modelling in diseases of the cardiovascular system, such as atherosclerosis. Various members of the MMP family have been shown to be expressed in atherosclerotic lesions, but MMP9 is consistently seen in inflammatory atherosclerotic lesions ...

    Matrix metalloproteinases (MMPs) and their inhibitors are important in connective tissue re-modelling in diseases of the cardiovascular system, such as atherosclerosis. Various members of the MMP family have been shown to be expressed in atherosclerotic lesions, but MMP9 is consistently seen in inflammatory atherosclerotic lesions. MMP9 over-expression is implicated in the vascular re-modelling events preceding plaque rupture (the most common cause of acute myocardial infarction). Reduced MMP9 activity, either by genetic manipulation or through pharmacological intervention, has an impact on ventricular re-modelling following infarction. MMP9 activity may therefore represent a key mechanism in the pathogenesis of heart failure. We have determined the crystal structure, at 2.3 A resolution, of the catalytic domain of human MMP9 bound to a peptidic reverse hydroxamate inhibitor as well as the complex of the same inhibitor bound to an active-site mutant (E402Q) at 2.1 A resolution. MMP9 adopts the typical MMP fold. The catalytic centre is composed of the active-site zinc ion, co-ordinated by three histidine residues (401, 405 and 411) and the essential glutamic acid residue (402). The main differences between the catalytic domains of various MMPs occur in the S1' subsite or selectivity pocket. The S1' specificity site in MMP9 is perhaps best described as a tunnel leading toward solvent, as in MMP2 and MMP13, as opposed to the smaller pocket found in fibroblast collagenase and matrilysin. The present structure enables us to aid the design of potent and specific inhibitors for this important cardiovascular disease target.

    Organizational Affiliation: 

    AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
92 KDA TYPE IV COLLAGENASEA, B163Homo sapiensMutation(s): 1 
Gene Names: MMP9, CLG4B
EC: 3.4.24.35
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
PHAROS:  P14780
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14780
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STN
Query on STN
Download Ideal Coordinates CCD File 
G [auth A],
O [auth B]		2-{[FORMYL(HYDROXY)AMINO]METHYL}-4-METHYLPENTANOIC ACID
C8 H15 N O4
LFMOJNDZFCHHPV-SSDOTTSWSA-N		 Ligand Interaction
BUM
Query on BUM
Download Ideal Coordinates CCD File 
H [auth A],
P [auth B]		2-AMINO-N,3,3-TRIMETHYLBUTANAMIDE
C7 H16 N2 O
BPKJNEIOHOEWLO-RXMQYKEDSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
Q [auth B],
R [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
K [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.523α = 90
b = 56.523β = 90
c = 263.761γ = 90
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance