6AHS | pdb_00006ahs

Mouse Kallikrein 7 in complex with imidazolinylindole derivative

• PDB DOI: https://doi.org/10.2210/pdb6AHS/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-20 Released: 2019-01-02 
• Deposition Author(s): Sugawara, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Discovery and structure-activity relationship of imidazolinylindole derivatives as kallikrein 7 inhibitors.

Murafuji, H., Muto, T., Goto, M., Imajo, S., Sugawara, H., Oyama, Y., Minamitsuji, Y., Miyazaki, S., Murai, K., Fujioka, H.

(2019) Bioorg Med Chem Lett 29: 334-338

• PubMed: 30522951 
• DOI: https://doi.org/10.1016/j.bmcl.2018.11.011
• Primary Citation Related Structures: 
  6AHS


• PubMed Abstract: 
  

  A series of imidazolinylindole derivatives were discovered as novel kallikrein 7 (KLK7, stratum corneum chymotryptic enzyme) inhibitors. Structure-activity relationship (SAR) studies led to the identification of potent human KLK7 inhibitors. By further modification of the benzenesulfonyl moiety to overcome species differences in inhibitory activity, potent inhibitors against both human and mouse KLK7 were identified. Furthermore, the complex structure of 25 with mouse KLK7 could explain the SAR and the cause of the species differences in inhibitory activity.

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Organizational Affiliation: 
• Asubio Pharma Co., Ltd, 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
Asubio Pharma Co., Ltd, 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan. Electronic address: [e-mail].
Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka 565-0871, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.22 kDa 
• Atom Count: 1,894 
• Modeled Residue Count: 224 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallikrein-7	A	224	Mus musculus	Mutation(s): 0  Gene Names: Klk7, Prss6, Scce EC: 3.4.21.117
UniProt
Find proteins for Q91VE3 (Mus musculus) Explore Q91VE3  Go to UniProtKB:  Q91VE3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9YO (Subject of Investigation/LOI)	B [auth A]	1-[(2-chlorophenyl)sulfonyl]-5-methyl-3-[(4R)-2-methyl-4,5-dihydro-1H-imidazol-4-yl]-1H-indole C19 H18 Cl N3 O2 S QKLXECCUITXSOU-KRWDZBQOSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.156	α = 90
b = 71.156	β = 90
c = 98.907	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-02 
Deposition Author(s): Sugawara, H.

Revision History  

• Version 1.0: 2019-01-02
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary