3EDZ

Crystal structure of catalytic domain of TACE with hydroxamate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of novel hydroxamates as highly potent tumor necrosis factor-alpha converting enzyme inhibitors. Part II: optimization of the S3' pocket.

Mazzola, R.D.Zhu, Z.Sinning, L.McKittrick, B.Lavey, B.Spitler, J.Kozlowski, J.Neng-Yang, S.Zhou, G.Guo, Z.Orth, P.Madison, V.Sun, J.Lundell, D.Niu, X.

(2008) Bioorg Med Chem Lett 18: 5809-5814

  • DOI: 10.1016/j.bmcl.2008.09.045
  • Primary Citation of Related Structures:  
    3E8R, 3EDZ

  • PubMed Abstract: 
  • A series of cyclopropyl hydroxamic acids were prepared. Many of the compounds displayed picomolar affinity for the TACE enzyme while maintaining good to excellent selectivity profiles versus MMP-1, -2, -3, -7, -14, and ADAM-10. X-ray analysis of an inhibitor in the TACE active site indicated that the molecules bound to the enzyme in the S1'-S3' pocket ...

    A series of cyclopropyl hydroxamic acids were prepared. Many of the compounds displayed picomolar affinity for the TACE enzyme while maintaining good to excellent selectivity profiles versus MMP-1, -2, -3, -7, -14, and ADAM-10. X-ray analysis of an inhibitor in the TACE active site indicated that the molecules bound to the enzyme in the S1'-S3' pocket.


    Organizational Affiliation

    Department of Medicinal Chemistry, Schering Plough Research Institute, Kenilworth, NJ 07033, USA. robert.mazzola@spcorp.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADAM 17 AB271Homo sapiensMutation(s): 3 
Gene Names: ADAM17CSVPTACE
EC: 3.4.24.86
Find proteins for P78536 (Homo sapiens)
Explore P78536 
Go to UniProtKB:  P78536
NIH Common Fund Data Resources
PHAROS:  P78536
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
550
Query on 550

Download Ideal Coordinates CCD File 
B
methyl (1R,2S)-2-(hydroxycarbamoyl)-1-{4-[(2-methylquinolin-4-yl)methoxy]benzyl}cyclopropanecarboxylate
C24 H24 N2 O5
HJWMYFBKJRVWJY-YKSBVNFPSA-N
 Ligand Interaction
INN
Query on INN

Download Ideal Coordinates CCD File 
A
N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide
C19 H37 N5 O5
LMIQCBIEAHJAMZ-GZBFAFLISA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
550Ki:  8   nM  BindingDB
550Ki:  8   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.796α = 90
b = 75.702β = 90
c = 102.877γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
BUSTER-TNTrefinement
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2013-02-27
    Changes: Other