3KEK

Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of (pyridin-4-yl)-2H-tetrazole as a novel scaffold to identify highly selective matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.

Schnute, M.E.O'Brien, P.M.Nahra, J.Morris, M.Howard Roark, W.Hanau, C.E.Ruminski, P.G.Scholten, J.A.Fletcher, T.R.Hamper, B.C.Carroll, J.N.Patt, W.C.Shieh, H.S.Collins, B.Pavlovsky, A.G.Palmquist, K.E.Aston, K.W.Hitchcock, J.Rogers, M.D.McDonald, J.Johnson, A.R.Munie, G.E.Wittwer, A.J.Man, C.F.Settle, S.L.Nemirovskiy, O.Vickery, L.E.Agawal, A.Dyer, R.D.Sunyer, T.

(2009) Bioorg.Med.Chem.Lett. 20: 576-580

  • DOI: 10.1016/j.bmcl.2009.11.081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Potent, highly selective and orally-bioavailable MMP-13 inhibitors have been identified based upon a (pyridin-4-yl)-2H-tetrazole scaffold. Co-crystal structure analysis revealed that the inhibitors bind at the S(1)(') active site pocket and are not l ...

    Potent, highly selective and orally-bioavailable MMP-13 inhibitors have been identified based upon a (pyridin-4-yl)-2H-tetrazole scaffold. Co-crystal structure analysis revealed that the inhibitors bind at the S(1)(') active site pocket and are not ligands for the catalytic zinc atom. Compound 29b demonstrated reduction of cartilage degradation biomarker (TIINE) levels associated with cartilage protection in a preclinical rat osteoarthritis model.


    Organizational Affiliation

    Global Research and Development, Pfizer Inc., 700 Chesterfield Parkway West, St. Louis, MO 63017, USA. mark.e.schnute@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagenase 3
A, B
167Homo 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
3EK
Query on 3EK

Download SDF File 
Download CCD File 
A, B
trans-4-[(3-{2-[(4-fluorobenzyl)carbamoyl]-6-methylpyridin-4-yl}-1H-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid
(1r,4r)-4-((3-(2((4-fluorobenzyl)carbamoyl)-6-methylpyridin-4-yl)-1h-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid
C24 H26 F N5 O3
PBYUEXSDWHTFAM-IYARVYRRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3EKKi: 4.4 nM BINDINGMOAD
3EKKi: 4.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.846α = 90.00
b = 95.740β = 90.00
c = 36.443γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description