1ZTQ

Crystal structure of the catalytic domain of MMP-13 complexed with WAY-033

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Identification of potent and selective MMP-13 inhibitors

Wu, J., Rush III, T.S., Hotchandani, R., Du, X., Geck, M., Collins, E., Xu, Z.B., Skotnicki, J., Levin, J.I., Lovering, F.E.

(2005) Bioorg Med Chem Lett 15: 4105-4109

  • DOI: https://doi.org/10.1016/j.bmcl.2005.06.019
  • Primary Citation of Related Structures:  
    1ZTQ

  • PubMed Abstract: 

    A potent, selective series of MMP-13 inhibitors has been derived from a weak (3.2 microM) inhibitor that did not bear a zinc chelator. Structure-based drug design strategies were employed to append a Zn-chelating group to one end of the molecule and functionality to enhance selectivity to the other. A compound from this series demonstrated rat oral bioavailability and efficacy in a bovine articular cartilage explant model.

    • Organizational Affiliation: 

    Department of Chemical and Screening Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagenase 3
A, B, C, D
165Homo sapiensMutation(s): 0 
Gene Names: MMP13
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
033
Query on 033
Download Ideal Coordinates CCD File 
BA [auth D],
J [auth A],
P [auth B],
V [auth C]		N-({4'-[(1-BENZOFURAN-2-YLCARBONYL)AMINO]-1,1'-BIPHENYL-4-YL}SULFONYL)-L-VALINE
C26 H24 N2 O6 S
HJFONKSERLWIGE-DEOSSOPVSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
Q [auth C]
E [auth A],
F [auth A],
K [auth B],
L [auth B],
Q [auth C],
R [auth C],
W [auth D],
X [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
AA [auth D]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
AA [auth D],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
Y [auth D],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
033 BindingDB:  1ZTQ IC50: min: 1.3, max: 2.4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.937α = 90
b = 135.252β = 104.95
c = 69.385γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-30
    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: 2024-02-14
    Changes: Data collection, Database references, Derived calculations