3EWJ

Crystal structure of catalytic domain of TACE with carboxylate inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3EWJ/pdb

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


• Deposited: 2008-10-15 Released: 2008-11-18 
• Deposition Author(s): Orth, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.210 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Discovery of novel spirocyclopropyl hydroxamate and carboxylate compounds as TACE inhibitors.

Guo, Z., Orth, P., Wong, S.C., Lavey, B.J., Shih, N.Y., Niu, X., Lundell, D.J., Madison, V., Kozlowski, J.A.

(2009) Bioorg Med Chem Lett 19: 54-57

• PubMed: 19054672 
• DOI: https://doi.org/10.1016/j.bmcl.2008.11.034
• Primary Citation of Related Structures:  
  3EWJ


• PubMed Abstract: 
  

  We have discovered nanomolar inhibitors of TNF-alpha convertase (TACE) comprised of a novel spirocyclic scaffold and either a carboxylate or hydroxamate zinc binding moiety. X-ray crystal structures and computer models of selected compounds binding to TACE explain the observed SAR. We report the first TACE X-ray crystal structure for an inhibitor with a carboxylate zinc ligand.

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Organizational Affiliation: 

Department of Chemistry, Schering-Plough Research Institute, Kenilworth, NJ 07033-0539, 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: 62.35 kDa 
• Atom Count: 4,497 
• Modelled Residue Count: 509 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAM 17	A, B	271	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
642	F [auth B]	(1S,3R,6S)-4-oxo-6-{4-[(2-phenylquinolin-4-yl)methoxy]phenyl}-5-azaspiro[2.4]heptane-1-carboxylic acid C29 H24 N2 O4 BFZXMIUWGSTUAL-ZSOKXDGFSA-N
INN	D [auth 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
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
642	PDBBind:  3EWJ	Ki: 143 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000919 (INN)	D [auth A]	3,N(D,L-[2-(HYDROXYAMINO-CARBONYL)METHYL]-4-METHYL PENTANOYL)L-3-(TERT-BUTYL)GLYCYL-L-ALANINE	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.210 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.398	α = 90
b = 76.176	β = 90
c = 103.565	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-18 
Deposition Author(s): Orth, P.

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2013-02-27
  Changes: Other
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary