3S0N

Crystal Structure of Human Chymase with Benzimidazolone Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3S0N/pdb

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


• Deposited: 2011-05-13 Released: 2011-07-20 
• Deposition Author(s): Qian, K.C., Farrow, N.A., Padyana, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.230 
• R-Value Work: 0.193 

Literature

Benzimidazolone as potent chymase inhibitor: Modulation of reactive metabolite formation in the hydrophobic (P(1)) region.

Lo, H.Y., Nemoto, P.A., Kim, J.M., Hao, M.H., Qian, K.C., Farrow, N.A., Albaugh, D.R., Fowler, D.M., Schneiderman, R.D., Michael August, E., Martin, L., Hill-Drzewi, M., Pullen, S.S., Takahashi, H., De Lombaert, S.

(2011) Bioorg Med Chem Lett 21: 4533-4539

• PubMed: 21733690 
• DOI: https://doi.org/10.1016/j.bmcl.2011.05.126
• Primary Citation of Related Structures:  
  3S0N


• PubMed Abstract: 
  

  A new class of chymase inhibitor featuring a benzimidazolone core with an acid side chain and a P(1) hydrophobic moiety is described. Incubation of the lead compound with GSH resulted in the formation of a GSH conjugate on the benzothiophene P(1) moiety. Replacement of the benzothiophene with different heterocyclic systems such as indoles and benzoisothiazole is feasible. Among the P(1) replacements, benzoisothiazole prevents the formation of GSH conjugate and an in silico analysis of oxidative potentials agreed with the experimental outcome.

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Organizational Affiliation: 

Boehringer Ingelheim Pharmaceuticals Inc., Medicinal Chemistry, Ridgefield, CT 06877, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 25.88 kDa 
• Atom Count: 1,982 
• Modelled Residue Count: 226 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymase	A	226	Homo sapiens	Mutation(s): 3  Gene Names: CMA1, CYH, CYM EC: 3.4.21.39
UniProt & NIH Common Fund Data Resources
Find proteins for P23946 (Homo sapiens) Explore P23946  Go to UniProtKB:  P23946
PHAROS:  P23946 GTEx:  ENSG00000092009

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0BB	E [auth A]	4-{3-[(4-methyl-1-benzothiophen-3-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}butanoic acid C21 H20 N2 O3 S WYBNXPWKJQJMLG-UHFFFAOYSA-N
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0BB	PDBBind:  3S0N	IC50: 180 (nM) from 1 assay(s)
	Binding MOAD:  3S0N	IC50: 180 (nM) from 1 assay(s)
	BindingDB:  3S0N	IC50: min: 97, max: 180 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.230 
• R-Value Work: 0.193 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.83	α = 90
b = 73.83	β = 90
c = 48.45	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Qian, K.C., Farrow, N.A., Padyana, A.K.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary