1XUD

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the highly selective inhibition of MMP-13.

Engel, C.K.Pirard, B.Schimanski, S.Kirsch, R.Habermann, J.Klingler, O.Schlotte, V.Weithmann, K.U.Wendt, K.U.

(2005) Chem.Biol. 12: 181-189

  • DOI: 10.1016/j.chembiol.2005.01.008
  • Primary Citation of Related Structures:  
  • Also Cited By: 3DPF, 3DPE, 3DNG

  • PubMed Abstract: 
  • The paradigm for matrix metalloprotease inhibition combines active site tailoring and catalytic zinc ligation. But, selectivity has been difficult. Now, Engel et al. present novel compounds, completely selective for MMP-13, with a unique binding mode ...

    The paradigm for matrix metalloprotease inhibition combines active site tailoring and catalytic zinc ligation. But, selectivity has been difficult. Now, Engel et al. present novel compounds, completely selective for MMP-13, with a unique binding mode.


    Organizational Affiliation

    Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880, USA




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
PB4
Query on PB4

Download SDF File 
Download CCD File 
A, B
N,N'-BIS(4-FLUORO-3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE
PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-(4-FLUORO-3-METHYL-BENZYLAMIDE)
C22 H20 F2 N4 O2
PYFRREJCFXFNRR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PB4IC50: 0.7 - 110 nM (100) BINDINGDB
PB4IC50: 8 nM BINDINGMOAD
PB4IC50: 8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.022α = 90.00
b = 36.475β = 130.41
c = 95.060γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CNSphasing
XDSdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance