6ASH | pdb_00006ash

Crystal structure of human Cathepsin K with a non-active site inhibitor at 1.42 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6ASH/pdb

• Classification: HYDROLASE/ HYDROLASE Inhibitor
• Organism(s): Homo sapiens
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2017-08-24 Released: 2018-08-29 
• Deposition Author(s): Law, S., Aguda, A., Nguyen, N., Brayer, G., Bromme, D.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.116 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Cathepsin K with a non-active site inhibitor at 1.42 Angstrom resolution.

Law, S., Brayer, G., Bromme, D.

To be published.

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: homology

Macromolecule Content 

• Total Structure Weight: 24.27 kDa 
• Atom Count: 1,982 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A	215	Homo sapiens	Mutation(s): 1  Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens) Explore P43235  Go to UniProtKB:  P43235
PHAROS:  P43235 GTEx:  ENSG00000143387

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1XF (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	2-{[(carbamoylsulfanyl)acetyl]amino}benzoic acid C10 H10 N2 O4 S NWUAPELPCMQTDN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1XF	BindingDB:  6ASH	IC50: 8.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.116 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.48	α = 90
b = 60.4	β = 95.12
c = 44.15	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Law, S., Aguda, A., Nguyen, N., Brayer, G., Bromme, D.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-89974
Canadian Institutes of Health Research (CIHR)	Canada	MOP-125866
Canadian Institutes of Health Research (CIHR)	Canada	MOP-125866
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-326803-13

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary