1XUR

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 

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
PB5
Query on PB5

Download SDF File 
Download CCD File 
A, B
N,N'-BIS(PYRIDIN-3-YLMETHYL)PYRIMIDINE-4,6-DICARBOXAMIDE
PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-[(PYRIDIN-3-YLMETHYL)-AMIDE]
C18 H16 N6 O2
NHPBWKYFMTXWAA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PB5IC50: 6600 nM (100) BINDINGDB
PB5IC50: 6600 nM BINDINGMOAD
PB5IC50: 6600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.508α = 90.00
b = 36.486β = 130.52
c = 95.586γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

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