5Y9L | pdb_00005y9l

Human kallikrein 7 in complex with 1,3,6-trisubstituted 1,4-diazepane-7-one

• PDB DOI: https://doi.org/10.2210/pdb5Y9L/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-25 Released: 2017-11-29 
• Deposition Author(s): Sugawara, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.276 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Discovery and structure-activity relationship study of 1,3,6-trisubstituted 1,4-diazepane-7-ones as novel human kallikrein 7 inhibitors

Murafuji, H., Sakai, H., Goto, M., Imajo, S., Sugawara, H., Muto, T.

(2017) Bioorg Med Chem Lett 27: 5272-5276

• PubMed: 29102227 
• DOI: https://doi.org/10.1016/j.bmcl.2017.10.030
• Primary Citation Related Structures: 
  5Y9L, 5YJK


• PubMed Abstract: 
  

  Compound 1, composed of a 1,3,6-trisubstituted 1,4-diazepane-7-one, was discovered as a novel human kallikrein 7 (KLK7, stratum corneum chymotryptic enzyme, SCCE) inhibitor, and its derivatives were synthesized and evaluated. Structure-activity relationship studies of the amidoxime unit and benzoic acid part of this new scaffold led to the identification of 25 and 34, which were more potent than the hit compound, 1. The X-ray co-crystal structure of compound 25 and human KLK7 revealed the characteristic interactions and enabled explanations of the structure-activity relationship.

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Organizational Affiliation: 
• Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: [e-mail].
Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: [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: 25.02 kDa 
• Atom Count: 1,809 
• 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	Homo sapiens	Mutation(s): 0  Gene Names: KLK7, PRSS6, SCCE EC: 3.4.21.117
UniProt & NIH Common Fund Data Resources
Find proteins for P49862 (Homo sapiens) Explore P49862  Go to UniProtKB:  P49862
PHAROS:  P49862 GTEx:  ENSG00000169035

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8R3	B [auth A]	3-[2-[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-(dimethylhydrazinylidene)-7-oxidanylidene-1,4-diazepan-1-yl]ethanoylamino]benzoic acid C24 H28 Cl N5 O5 STRUTOBZXDUGAL-QGZVFWFLSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
8R3	BindingDB:  5Y9L	IC50: 1900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.276 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.895	α = 90
b = 90.926	β = 90
c = 92.03	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: 2017-11-29 
Deposition Author(s): Sugawara, H.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary