6YYO

Structure of Cathepsin S in complex with Compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.137 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin SA [auth AAA],
B [auth BBB]
225Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25774
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q1K (Subject of Investigation/LOI)
Query on Q1K

Download Ideal Coordinates CCD File 
PA [auth BBB],
S [auth AAA]
6-(4-methylsulfonylpiperazin-1-yl)-[1,2,4]triazolo[4,3-b]pyridazine
C10 H14 N6 O2 S
UNYVOSROGSXTRY-UHFFFAOYSA-N
FLC
Query on FLC

Download Ideal Coordinates CCD File 
U [auth BBB]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth AAA],
T [auth BBB],
V [auth BBB],
W [auth BBB]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
H [auth AAA]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth BBB]
BA [auth BBB]
CA [auth BBB]
D [auth AAA]
DA [auth BBB]
AA [auth BBB],
BA [auth BBB],
CA [auth BBB],
D [auth AAA],
DA [auth BBB],
E [auth AAA],
EA [auth BBB],
F [auth AAA],
FA [auth BBB],
G [auth AAA],
GA [auth BBB],
HA [auth BBB],
I [auth AAA],
IA [auth BBB],
J [auth AAA],
JA [auth BBB],
K [auth AAA],
KA [auth BBB],
L [auth AAA],
LA [auth BBB],
M [auth AAA],
MA [auth BBB],
N [auth AAA],
NA [auth BBB],
O [auth AAA],
OA [auth BBB],
P [auth AAA],
Q [auth AAA],
R [auth AAA],
X [auth BBB],
Y [auth BBB],
Z [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Q1K BindingDB:  6YYO Kd: 9.60e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.137 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.458α = 90
b = 85.458β = 90
c = 150.899γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2024-11-13
    Changes: Structure summary