4D8N

Human Kallikrein 6 Inhibitors with a para-Amidobenzylanmine P1 Group Carry a High Binding Efficiency

• PDB DOI: https://doi.org/10.2210/pdb4D8N/pdb

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


• Deposited: 2012-01-11 Released: 2012-03-21 
• Deposition Author(s): Chen, X., Xia, T., Wang, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.208 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Human kallikrein 6 inhibitors with a para-amidobenzylanmine P1 group identified through virtual screening.

Liang, G., Chen, X., Aldous, S., Pu, S.F., Mehdi, S., Powers, E., Xia, T., Wang, R.

(2012) Bioorg Med Chem Lett 22: 2450-2455

• PubMed: 22386244 
• DOI: https://doi.org/10.1016/j.bmcl.2012.02.014
• Primary Citation of Related Structures:  
  4D8N


• PubMed Abstract: 
  

  A series of hK6 inhibitors with a para-amidobenzylamine P1 group and a 2-hydroxybenzamide scaffold linker was discovered through virtual screening. The X-ray structure of hK6 complexed with compound 9b was determined to a resolution of 1.68Å. The tertiary folding of the hK6 complexed with the inhibitor is conserved relative to the structure of the apo-protein, whereas the interaction between hK6 and the inhibitor is consistent with both the SAR and the in silico model used in the virtual screening.

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Organizational Affiliation: 

Molecular Innovative Therapeutics, Sanofi Pharmaceuticals, Bridgewater, NJ, 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: 24.83 kDa 
• Atom Count: 1,949 
• Modelled Residue Count: 222 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallikrein-6	A	223	Homo sapiens	Mutation(s): 3  Gene Names: KLK6, PRSS18, PRSS9 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q92876 (Homo sapiens) Explore Q92876  Go to UniProtKB:  Q92876
PHAROS:  Q92876 GTEx:  ENSG00000167755

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0HM	B [auth A]	2-{[4-(aminomethyl)phenyl]carbamoyl}-1-[(1-benzyl-1H-imidazol-2-yl)methyl]-3-hydroxypyridinium C24 H24 N5 O2 DMRCMJXUFJLJKH-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
0HM	PDBBind:  4D8N	IC50: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.208 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.185	α = 90
b = 45.95	β = 90
c = 109.077	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Chen, X., Xia, T., Wang, R.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary