4KP0

Crystal Structure of the human Chymase with TJK002


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


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Literature

Crystal structure of a complex of human chymase with its benzimidazole derived inhibitor

Matsumoto, Y.Kakuda, S.Koizumi, M.Mizuno, T.Muroga, Y.Kawamura, T.Takimoto-Kamimura, M.

(2013) J.SYNCHROTRON RADIAT. 20: 914-918

  • DOI: 10.1107/S0909049513020748

  • PubMed Abstract: 
  • The crystal structure of human chymase complexed with a novel benzimidazole inhibitor, TJK002, was determined at 2.8 Å resolution. The X-ray crystallographic study shows that the benzimidazole inhibitor forms a non-covalent interaction with the catal ...

    The crystal structure of human chymase complexed with a novel benzimidazole inhibitor, TJK002, was determined at 2.8 Å resolution. The X-ray crystallographic study shows that the benzimidazole inhibitor forms a non-covalent interaction with the catalytic domain of human chymase. The hydrophobic fragment of the inhibitor occupies the S1 pocket. The carboxylic acid group of the inhibitor forms hydrogen bonds with the imidazole N(ℇ) atom of His57 and/or the O(γ) atom of Ser195 which are members of the catalytic triad. This imidazole ring of His57 induces π-π stacking to the benzene ring of the benzimidazole scaffold as P2 moiety. Fragment molecular orbital calculation of the atomic coordinates by X-ray crystallography shows that this imidazole ring of His57 could be protonated with the carboxyl group of Asp102 or hydroxyl group of Ser195 and the stacking interaction is stabilized. A new drug design strategy is proposed where the stacking to the protonated imidazole of the drug target protein with the benzimidazole scaffold inhibitor causes unpredicted potent inhibitory activity for some enzymes.


    Organizational Affiliation

    Teijin Institute for Bio-medical Research, 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chymase
A
226Homo sapiensMutation(s): 0 
Gene Names: CMA1 (CYH, CYM)
EC: 3.4.21.39
Find proteins for P23946 (Homo sapiens)
Go to Gene View: CMA1
Go to UniProtKB:  P23946
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KPK
Query on KPK

Download SDF File 
Download CCD File 
A
4-({1-[(4-methyl-1-benzothiophen-3-yl)methyl]-1H-benzimidazol-2-yl}sulfanyl)butanoic acid
C21 H20 N2 O2 S2
YSOMBHFITHOMPW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KPKIC50: 22 nM (100) BINDINGDB
KPKKi: 2.24 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.226 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 56.920α = 90.00
b = 56.920β = 90.00
c = 177.490γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release