3KEC

Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.169 

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.

(2010) 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAE
Query on HAE

Download SDF File 
Download CCD File 
A, B
ACETOHYDROXAMIC ACID
C2 H5 N O2
RRUDCFGSUDOHDG-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
3KE
Query on 3KE

Download SDF File 
Download CCD File 
A, B
4-{[({3-[2-(4-methoxybenzyl)-2H-tetrazol-5-yl]phenyl}carbonyl)amino]methyl}benzoic acid
4-((3-(2-(4-methoxybenzyl)-2H-tetrazol-5-yl)benzamido)methyl)benzoic acid
C24 H21 N5 O4
VUTBCSIBPMXNCZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3KEIC50: 58 - 130 nM (100) BINDINGDB
3KEIC50: 130 nM BINDINGMOAD
3KEIC50: 58 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 133.209α = 90.00
b = 72.348β = 90.00
c = 36.356γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

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