4A6L | pdb_00004a6l

beta-tryptase inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4A6L/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2011-11-04 Released: 2012-01-25 
• Deposition Author(s): Mathieu, M., Maignan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.211 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: other

Literature

Structure-Based Library Design and the Discovery of a Potent and Selective Mast Cell Beta-Tryptase Inhibitor as an Oral Therapeutic Agent.

Liang, G., Aldous, S., Merriman, G., Levell, J., Pribish, J., Cairns, J., Chen, X., Maignan, S., Mathieu, M., Tsay, J., Sides, K., Rebello, S., Whitely, B., Morize, I., Pauls, H.W.

(2012) Bioorg Med Chem Lett 22: 1049

• PubMed: 22192588 
• DOI: https://doi.org/10.1016/j.bmcl.2011.11.119
• Primary Citation Related Structures: 
  4A6L


• PubMed Abstract: 
  

  A solid phase combinatorial library was designed based on X-ray structures and in-silico models to explore an inducible S4+ pocket, which is formed by a simple side-chain rotation of Tyr95. This inducible S4+ pocket is unique to β-tryptase and does not exist for other trypsin-like serine proteases of interest. Therefore, inhibitors utilizing this pocket have inherent advantages for being selective against other proteases in the same family. A member of this library was found to be a potent and selective β-tryptase inhibitor with a suitable pharmacokinetic profile for further clinical evaluation.

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Organizational Affiliation: 
• Molecular Innovative Therapeutics, Sanofi Pharmaceuticals, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 111.58 kDa 
• Atom Count: 8,134 
• Modeled Residue Count: 972 
• Deposited Residue Count: 980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPTASE ALPHA/BETA-1	A, B, C, D	245	Homo sapiens	Mutation(s): 0  EC: 3.4.21.59
UniProt & NIH Common Fund Data Resources
Find proteins for P20231 (Homo sapiens) Explore P20231  Go to UniProtKB:  P20231
PHAROS:  P20231 GTEx:  ENSG00000197253

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P43	E [auth A], F [auth B], G [auth C], H [auth D]	1-{3-[1-({5-[(2-fluorophenyl)ethynyl]furan-2-yl}carbonyl)piperidin-4-yl]phenyl}methanamine C25 H23 F N2 O2 FTLQSQQQFMZPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.211 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.234	α = 90
b = 82.234	β = 90
c = 170.654	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Mathieu, M., Maignan, S.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary