1XUD

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.chembiol.2005.01.008
  • Primary Citation of Related Structures:  
    1XUD, 1XUR

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagenase 3
A, B
171Homo sapiensMutation(s): 0 
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens)
Explore P45452 
Go to UniProtKB:  P45452
PHAROS:  P45452
GTEx:  ENSG00000137745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45452
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PB4
Query on PB4

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
N,N'-BIS(4-FLUORO-3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE
C22 H20 F2 N4 O2
PYFRREJCFXFNRR-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PB4 PDBBind:  1XUD IC50: 8 (nM) from 1 assay(s)
BindingDB:  1XUD IC50: min: 0.67, max: 110 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 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
b = 36.475β = 130.412
c = 95.06γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations