1ZXC | pdb_00001zxc

Crystal structure of catalytic domain of TNF-alpha converting enzyme (TACE) with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1ZXC/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-07 Released: 2005-09-27 
• Deposition Author(s): Levin, J.I., Chen, J.M., Laakso, L.M., Du, M., Schmid, J., Xu, W., Cummons, T., Xu, J., Zhang, Y., Jin, G., Cowling, R., Barone, D., Skotnicki, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.285 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Acetylenic TACE inhibitors. Part 2: SAR of six-membered cyclic sulfonamide hydroxamates.

Levin, J.I., Chen, J.M., Laakso, L.M., Du, M., Du, X., Venkatesan, A.M., Sandanayaka, V., Zask, A., Xu, J., Xu, W., Zhang, Y., Skotnicki, J.S.

(2005) Bioorg Med Chem Lett 15: 4345-4349

• PubMed: 16084720 
• DOI: https://doi.org/10.1016/j.bmcl.2005.06.072
• Primary Citation Related Structures: 
  1ZXC


• PubMed Abstract: 
  

  The SAR of a series of potent sulfonamide hydroxamate TACE inhibitors bearing a butynyloxy P1' group was explored. In particular, compound 5k has excellent in vitro potency against TACE enzyme and in cells, and oral activity in an in vivo model of TNF-alpha production and a collagen-induced arthritis model.

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Organizational Affiliation: 
• Wyeth Research, 401N. Middletown Road, Pearl River, NY 10965, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.4 kDa 
• Atom Count: 4,327 
• Modeled Residue Count: 517 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAM 17	A, B	263	Homo sapiens	Mutation(s): 2  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
IH6	D [auth A], F [auth B]	(3S)-4-{[4-(BUT-2-YNYLOXY)PHENYL]SULFONYL}-N-HYDROXY-2,2-DIMETHYLTHIOMORPHOLINE-3-CARBOXAMIDE C17 H22 N2 O5 S2 CVZIHNYAZLXRRS-HNNXBMFYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IH6	BindingDB:  1ZXC	IC50: min: 8, max: 9 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.285 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.12	α = 90
b = 59.17	β = 90
c = 195.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Levin, J.I., Chen, J.M., Laakso, L.M., Du, M., Schmid, J., Xu, W., Cummons, T., Xu, J., Zhang, Y., Jin, G., Cowling, R., Barone, D., Skotnicki, J.S.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary