3LIR

Human MMP12 in complex with non-zinc chelating inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights from selective non-phosphinic inhibitors of MMP-12 tailored to fit with an S1' loop canonical conformation.

Devel, L.Garcia, S.Czarny, B.Beau, F.LaJeunesse, E.Vera, L.Georgiadis, D.Stura, E.Dive, V.

(2010) J.Biol.Chem. 285: 35900-35909

  • DOI: 10.1074/jbc.M110.139634
  • Primary Citation of Related Structures:  3LIK, 3LIL, 3LJG

  • PubMed Abstract: 
  • After the disappointment of clinical trials with early broad spectrum synthetic inhibitors of matrix metalloproteinases (MMPs), the field is now resurging with a new focus on the development of selective inhibitors that fully discriminate between dif ...

    After the disappointment of clinical trials with early broad spectrum synthetic inhibitors of matrix metalloproteinases (MMPs), the field is now resurging with a new focus on the development of selective inhibitors that fully discriminate between different members of the MMP family with several therapeutic applications in perspective. Here, we report a novel class of highly selective MMP-12 inhibitors, without a phosphinic zinc-binding group, designed to plunge deeper into the S(1)' cavity of the enzyme. The best inhibitor from this series, identified through a systematic chemical exploration, displays nanomolar potency toward MMP-12 and selectivity factors that range between 2 and 4 orders of magnitude toward a large set of MMPs. Comparison of the high resolution x-ray structures of MMP-12 in free state or bound to this new MMP-12 selective inhibitor reveals that this compound fits deeply within the S(1)' specificity cavity, maximizing surface/volume ratios, without perturbing the S(1)' loop conformation. This is in contrast with highly selective MMP-13 inhibitors that were shown to select a particular S(1)' loop conformation. The search for such compounds that fit precisely to preponderant S(1)' loop conformation of a particular MMP may prove to be an alternative effective strategy for developing selective inhibitors of MMPs.


    Organizational Affiliation

    Commissariat à l'Energie Atomique, Service d'Ingénierie Moléculaire de Protéines, CE-Saclay, 91191 Gif/Yvette Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
159Homo sapiensGene 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GLY
Query on GLY

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Download CCD File 
A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EEC
Query on EEC

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Download CCD File 
A
N-[3-(3-phenylisoxazol-5-yl)propanoyl]-L-alpha-glutamyl-L-alpha-glutamyl-amide
C22 H26 N4 O8
LIIRZRQVACDFBI-HOTGVXAUSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000800 (EEC)
Query on PRD_000800
AN-[3-(3-PHENYLISOXAZOL-5-YL)PROPANOYL]-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMYL-AMIDEPeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EECKi: 119 nM (99) BINDINGDB
EECKi: 119 nM BINDINGMOAD
EECKi: 119 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.997α = 90.00
b = 63.171β = 90.00
c = 37.573γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
REFMACphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-12-12
    Type: Other