3L0V

Crystal structure of catalytic domain of TACE with the first hydantoin inhibitor occupying the S1' pocket

• PDB DOI: https://doi.org/10.2210/pdb3L0V/pdb

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


• Deposited: 2009-12-10 Released: 2010-03-02 
• Deposition Author(s): Orth, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.208 
• R-Value Work: 0.189 

Starting Model: experimental

Literature

Discovery and SAR of hydantoin TACE inhibitors.

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

(2010) Bioorg Med Chem Lett 20: 1877-1880

• PubMed: 20172725 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.148
• Primary Citation of Related Structures:  
  3L0T, 3L0V


• PubMed Abstract: 
  

  We disclose inhibitors of TNF-alpha converting enzyme (TACE) designed around a hydantoin zinc binding moiety. Crystal structures of inhibitors bound to TACE revealed monodentate coordination of the hydantoin to the zinc. SAR, X-ray, and modeling designs are described. To our knowledge, these are the first reported X-ray structures of TACE with a hydantoin zinc ligand.

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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: 61.85 kDa 
• Atom Count: 4,288 
• Modelled Residue Count: 507 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
724	D [auth A], F [auth B]	(5R)-5-[(5-methoxy-3-oxo-1,3-dihydro-2H-indazol-2-yl)methyl]-5-methylimidazolidine-2,4-dione C13 H14 N4 O4 PIEMRKVLYXWKFP-CYBMUJFWSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
724	BindingDB:  3L0V	Ki: 23 (nM) from 1 assay(s)
	PDBBind:  3L0V	Ki: 23 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.208 
• R-Value Work: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.038	α = 90
b = 76.836	β = 90
c = 103.798	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: 2010-03-02 
Deposition Author(s): Orth, P.

Revision History  

• Version 1.0: 2010-03-02
  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