3B92

Novel thio-based TACE inhibitors Part 2: Rational design, synthesis and SAR of thiol-contaning aryl sufones

• PDB DOI: https://doi.org/10.2210/pdb3B92/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2007-11-02 Released: 2007-12-18 
• Deposition Author(s): Wei, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.238 

Starting Model: experimental

Literature

Novel thiol-based TACE inhibitors. Part 2: Rational design, synthesis, and SAR of thiol-containing aryl sulfones.

Bandarage, U.K., Wang, T., Come, J.H., Perola, E., Wei, Y., Rao, B.G.

(2008) Bioorg Med Chem Lett 18: 44-48

• PubMed: 18054488 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.014
• Primary Citation of Related Structures:  
  3B92


• PubMed Abstract: 
  

  A series of potent thiol-containing aryl sulfone TACE inhibitors were designed and synthesized. The SAR and MMP selectivity of the series were investigated. In particular, compound 8b showed excellent in vitro potency against the isolated enzyme and good selectivity over MMP-2, -7, -8, -9, and -13. The X-ray structure of 8b in complex with TACE was also obtained.

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Organizational Affiliation: 

Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.65 kDa 
• Atom Count: 2,317 
• Modelled Residue Count: 259 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAM 17	A	259	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
440	D [auth A]	3-{[4-(but-2-yn-1-yloxy)phenyl]sulfonyl}propane-1-thiol C13 H16 O3 S2 CARKQNSZFCLNKM-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
440	PDBBind:  3B92	Ki: 10 (nM) from 1 assay(s)
	BindingDB:  3B92	Ki: min: 10, max: 10 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.238 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.72	α = 90
b = 76.72	β = 90
c = 105.93	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Wei, Y.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary