3LEA

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

• PDB DOI: https://doi.org/10.2210/pdb3LEA/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


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

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 20663669 
• DOI: https://doi.org/10.1016/j.bmcl.2010.06.134
• Primary Citation of Related Structures:  
  3LE9, 3LEA


• 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.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, Kenilworth, NJ 07033, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.18 kDa 
• Atom Count: 4,557 
• Modelled Residue Count: 519 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disintegrin and metalloproteinase domain-containing protein 17	A, B	270	Homo sapiens	Mutation(s): 3  Gene Names: ADAM17, CSVP, TACE 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 GTEx:  ENSG00000151694

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z93	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
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA	E [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z93	PDBBind:  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 = 102.481	α = 90
b = 112.54	β = 90
c = 51.272	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary