5D2B

Crystal structure of a mutated catalytic domain of Human MMP12 in complex with an hydroxamate analogue of RXP470

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played by the Zinc-Binding Group on Potency and Selectivity.

Rouanet-Mehouas, C., Czarny, B., Beau, F., Cassar-Lajeunesse, E., Stura, E.A., Dive, V., Devel, L.

(2017) J. Med. Chem. 60: 403-414

  • DOI: 10.1021/acs.jmedchem.6b01420
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The most exploited strategy to develop potent zinc-metalloprotease inhibitors relies on a core zinc chelator and a peptidic or nonpeptidic scaffold that provides supplementary interactions for optimized potency and selectivity. Applied to matrix meta ...

    The most exploited strategy to develop potent zinc-metalloprotease inhibitors relies on a core zinc chelator and a peptidic or nonpeptidic scaffold that provides supplementary interactions for optimized potency and selectivity. Applied to matrix metalloproteases (MMPs) with highly conserved catalytic domains, this strategy failed to identify inhibitors with the desired selectivity profiles. To question the precise role of the zinc-binding group (ZBG), we have carried out a study on MMP-12 inhibitors with a common peptidic core but different ZBGs. We find that exchanging the ZBG modifies inhibitor positioning and affects its dynamics and selectivity. The binding properties of these compounds were compared through biochemical, structural, and calorimetric studies, showing a complex interplay between cooperative interactions and dynamics dictated by the ZBG. Improving selectivity will require expanding the ZBG repertoire within inhibitor libraries, since relying on a single ZBG significantly decreases our chance to identify effective inhibitors.

    Organizational Affiliation: 

    Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay , Gif/Yvette F-91191, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
159Homo sapiensMutation(s): 1 
Gene Names: MMP12 (HME)
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Go to Gene View: MMP12
Go to UniProtKB:  P39900
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
56O
Query on 56O
Download SDF File 
Download CCD File 
A
N-[(2R)-2-{[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol-5-yl]methyl}-4-(hydroxyamino)-4-oxobutanoyl]-L-alpha-glutamyl-L-alpha-glutamine
C30 H32 Cl N5 O10
VBMQORMYXJZHKU-OIBXWCBGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.900α = 90.00
b = 63.100β = 90.00
c = 36.790γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
MxCuBEdata collection
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2017-01-11
    Type: Database references
  • Version 1.3: 2017-01-25
    Type: Database references
  • Version 1.4: 2017-12-20
    Type: Structure summary