2ZA5 | pdb_00002za5

Crystal Structure of human tryptase with potent non-peptide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2ZA5/pdb

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


• Deposited: 2007-10-02 Released: 2008-02-26 
• Deposition Author(s): Spurlino, J.C., Barnakov, S.A., Lewandowski, F., Milligan, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.233 (Depositor) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Potent, nonpeptide inhibitors of human mast cell tryptase. Synthesis and biological evaluation of novel spirocyclic piperidine amide derivatives

Costanzo, M.J., Yabut, S.C., Zhang, H.-C., White, K.B., de Garavilla, L., Wang, Y., Minor, L.K., Tounge, B.A., Barnakov, A.N., Lewandowski, F., Milligan, C., Spurlino, J.C., Abraham, W.M., Boswell-Smith, V., Page, C.P., Maryanoff, B.E.

(2008) Bioorg Med Chem Lett 18: 2114-2121

• PubMed: 18272363 
• DOI: https://doi.org/10.1016/j.bmcl.2008.01.093
• Primary Citation Related Structures: 
  2ZA5, 2ZEB, 2ZEC


• PubMed Abstract: 
  

  We have explored a series of spirocyclic piperidine amide derivatives (5) as tryptase inhibitors. Thus, 4 (JNJ-27390467) was identified as a potent, selective tryptase inhibitor with oral efficacy in two animal models of airway inflammation (sheep and guinea pig asthma models). An X-ray co-crystal structure of 4 x tryptase revealed a hydrophobic pocket in the enzyme's active site, which is induced by the phenylethynyl group and is comprised of amino acid residues from two different monomers of the tetrameric protein.

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Organizational Affiliation: 
• Research and Early Development, Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, PA 19477-0776, 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: 111.62 kDa 
• Atom Count: 8,202 
• Modeled Residue Count: 972 
• Deposited Residue Count: 980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptase beta 2	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
2FF	E [auth A], F [auth B], G [auth C], H [auth D]	(5-(aminomethyl)-2H-spiro[benzofuran-3,4'-piperidine]-1'-yl)(5-(phenylethynyl)furan-2-yl)methanone C26 H24 N2 O3 YKTUSHSSKIWDRY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.233 (Depositor) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.678	α = 90
b = 82.678	β = 90
c = 170.284	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Spurlino, J.C., Barnakov, S.A., Lewandowski, F., Milligan, C.

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary