3LEA

Crystal structure of the catalytic domain of TACE with Isoindolinone-biphenyl-hydantoin inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Biaryl substituted hydantoin compounds as TACE inhibitors.

Yu, W.Tong, L.Kim, S.H.Wong, M.K.Chen, L.Yang, D.Y.Shankar, B.B.Lavey, B.J.Zhou, G.Kosinski, A.Rizvi, R.Li, D.Feltz, R.J.Piwinski, J.J.Rosner, K.E.Shih, N.Y.Siddiqui, M.A.Guo, Z.Orth, P.Shah, H.Sun, J.Umland, S.Lundell, D.J.Niu, X.Kozlowski, J.A.

(2010) Bioorg Med Chem Lett 20: 5286-5289

  • DOI: 10.1016/j.bmcl.2010.06.134
  • Primary Citation of Related Structures:  
    3LEA, 3LE9

  • PubMed Abstract: 
  • We disclose further optimization of hydantoin TNF-alpha convertase enzyme (TACE) inhibitors. SAR with respect to the non-prime region of TACE active site was explored. A series of biaryl substituted hydantoin compounds was shown to have sub-nanomolar K(i), good rat PK, and good selectivity versus MMP-1, -2, -3, -7, -9, and -13 ...

    We disclose further optimization of hydantoin TNF-alpha convertase enzyme (TACE) inhibitors. SAR with respect to the non-prime region of TACE active site was explored. A series of biaryl substituted hydantoin compounds was shown to have sub-nanomolar K(i), good rat PK, and good selectivity versus MMP-1, -2, -3, -7, -9, and -13.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, Kenilworth, NJ 07033, USA. wensheng.yu@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Disintegrin and metalloproteinase domain-containing protein 17A, B270Homo sapiensMutation(s): 3 
Gene Names: ADAM17CSVPTACE
EC: 3.4.24.86
UniProt & NIH Common Fund Data Resources
Find proteins for P78536 (Homo sapiens)
Explore P78536 
Go to UniProtKB:  P78536
PHAROS:  P78536
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z93 (Subject of Investigation/LOI)
Query on Z93

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]2-{[(4R)-2,5-dioxo-4-(4-pyridin-3-ylphenyl)imidazolidin-4-yl]methyl}-6-methoxy-1-oxo-1H-isoindolium
C24 H19 N4 O4
IPWWTFLYEBQOPS-DEOSSOPVSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
E [auth B]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Z93 PDBBind:  3LEA Ki: 0.8 (nM) from 1 assay(s)
Binding MOAD:  3LEA Ki: 0.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.481α = 90
b = 112.54β = 90
c = 51.272γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2010-01-14 
  • Released Date: 2010-12-08 
  • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance