6YYP

Structure of Cathepsin S in complex with Compound 2

• PDB DOI: https://doi.org/10.2210/pdb6YYP/pdb

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


• Deposited: 2020-05-05 Released: 2021-05-12 
• Deposition Author(s): Wagener, M., Schade, M., Merla, B., Hars, U., Kueckelhaus, S.Q.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.188 
• R-Value Work: 0.141 

Starting Model: experimental

Literature

Highly Selective Sub-Nanomolar Cathepsin S Inhibitors by Merging Fragment Binders with Nitrile Inhibitors.

Schade, M., Merla, B., Lesch, B., Wagener, M., Timmermanns, S., Pletinckx, K., Hertrampf, T.

(2020) J Med Chem 63: 11801-11808

• PubMed: 32880457 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c00949
• Primary Citation of Related Structures:  
  6YYN, 6YYO, 6YYP, 6YYQ, 6YYR


• PubMed Abstract: 
  

  Pharmacological inhibition of cathepsin S (CatS) allows for a specific modulation of the adaptive immune system and many major diseases. Here, we used NMR fragment screening and crystal structure-aided merging to synthesize novel, highly selective CatS inhibitors with picomolar enzymatic Ki values and nanomolar functional activity in human Raji cells. Noncovalent fragment hits revealed binding hotspots, while the covalent inhibitor structure-activity relationship enabled efficient potency optimization.

---

Organizational Affiliation: 

Grünenthal GmbH, Zieglerstr. 6, 52078 Aachen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 51.21 kDa 
• Atom Count: 3,993 
• Modelled Residue Count: 442 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A [auth AAA], B [auth BBB]	225	Homo sapiens	Mutation(s): 0  Gene Names: CTSS EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens) Explore P25774  Go to UniProtKB:  P25774
PHAROS:  P25774 GTEx:  ENSG00000163131

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q1H (Subject of Investigation/LOI)	E [auth AAA]	1-(furan-2-ylmethyl)-5-(trifluoromethyl)benzimidazol-2-amine C13 H10 F3 N3 O QYVPLFHAOLRMBY-UHFFFAOYSA-N
SIN	F [auth BBB]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
MLA	G [auth BBB], H [auth BBB]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
ACT	C [auth AAA], D [auth AAA], I [auth BBB], J [auth BBB], K [auth BBB], L [auth BBB]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.188 
• R-Value Work: 0.141 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.689	α = 90
b = 118.689	β = 90
c = 205.586	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Wagener, M., Schade, M., Merla, B., Hars, U., Kueckelhaus, S.Q.

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2022-11-23
  Changes: Database references, Derived calculations
• Version 1.2: 2024-05-01
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary