5BPA

X-RAY Co-structure of MMP-13 with 4-[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}formamido)methyl]benzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fragment-based discovery of indole inhibitors of matrix metalloproteinase-13.

Taylor, S.J.Abeywardane, A.Liang, S.Muegge, I.Padyana, A.K.Xiong, Z.Hill-Drzewi, M.Farmer, B.Li, X.Collins, B.Li, J.X.Heim-Riether, A.Proudfoot, J.Zhang, Q.Goldberg, D.Zuvela-Jelaska, L.Zaher, H.Li, J.Farrow, N.A.

(2011) J. Med. Chem. 54: 8174-8187

  • DOI: 10.1021/jm201129m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Matrix metalloproteases (MMPs) play an important role in cartilage homeostasis under both normal and inflamed disease states and, thus, have become attractive targets for the treatment of arthritic diseases. Herein, we describe the identification of ...

    Matrix metalloproteases (MMPs) play an important role in cartilage homeostasis under both normal and inflamed disease states and, thus, have become attractive targets for the treatment of arthritic diseases. Herein, we describe the identification of a potent, selective MMP-13 inhibitor, developed using fragment-based structure-guided lead identification and optimization techniques. Virtual screening methods identified a novel, indole-based MMP-13 inhibitor that bound into the S1' pocket of the protein exhibiting a novel interaction pattern hitherto not observed in MMP-13 inhibitors. X-ray crystallographic structures were used to guide the elaboration of the fragment, ultimately leading to a potent inhibitor that was >100-fold selective over nine other MMP isoforms tested.


    Organizational Affiliation

    Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, Connecticut 06877-0368, United States. steven.taylor@boehringeringelheim.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagenase 3
A, B
171Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24.-
Find proteins for P45452 (Homo sapiens)
Go to Gene View: MMP13
Go to UniProtKB:  P45452
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
4UF
Query on 4UF

Download SDF File 
Download CCD File 
A, B
4-{[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}carbonyl)amino]methyl}benzoic acid
C24 H22 N4 O5
MMJPVSDTLGFIQW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4UFIC50: 0.8 - 31 nM (93) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.281α = 90.00
b = 36.141β = 131.48
c = 96.097γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Experimental preparation
  • Version 1.2: 2016-07-20
    Type: Data collection