6YYO | pdb_00006yyo

Structure of Cathepsin S in complex with Compound 1

PDB DOI: https://doi.org/10.2210/pdb6YYO/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: 1.50 Å
R-Value Free:
0.169 (Depositor), 0.169 (DCC)
R-Value Work:
0.137 (Depositor), 0.137 (DCC)

Starting Model: experimental
View more details

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

PubMed: 32880457 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.0c00949
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 53.41 kDa
Atom Count: 4,477
Modeled Residue Count: 440
Deposited Residue Count: 450
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25774
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q1K (Subject of Investigation/LOI) Query on Q1K Download:Ideal Coordinates CCD File SDF format, chain PA [auth BBB] SDF format, chain S [auth AAA] MOL2 format, chain PA [auth BBB] MOL2 format, chain S [auth AAA] mmCIF format, chain PA [auth BBB] mmCIF format, chain S [auth AAA]	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		Interactions Focus chain PA [auth BBB] Focus chain S [auth AAA] Interactions & Density Focus chain PA [auth BBB] Focus chain S [auth AAA]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain U [auth BBB] MOL2 format, chain U [auth BBB] mmCIF format, chain U [auth BBB]	U [auth BBB]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain U [auth BBB] Interactions & Density Focus chain U [auth BBB]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth BBB] SDF format, chain V [auth BBB] SDF format, chain T [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain W [auth BBB] MOL2 format, chain V [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain W [auth BBB] mmCIF format, chain V [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain C [auth AAA]	C [auth AAA], T [auth BBB], V [auth BBB], W [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth AAA] Focus chain T [auth BBB] Focus chain V [auth BBB] Focus chain W [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain T [auth BBB] Focus chain V [auth BBB] Focus chain W [auth BBB]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain H [auth AAA]	H [auth AAA]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Interactions & Density Focus chain H [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain BA [auth BBB] SDF format, chain CA [auth BBB] SDF format, chain D [auth AAA] SDF format, chain DA [auth BBB] SDF format, chain E [auth AAA] SDF format, chain EA [auth BBB] SDF format, chain F [auth AAA] SDF format, chain FA [auth BBB] SDF format, chain G [auth AAA] SDF format, chain GA [auth BBB] SDF format, chain HA [auth BBB] SDF format, chain I [auth AAA] SDF format, chain IA [auth BBB] SDF format, chain J [auth AAA] SDF format, chain JA [auth BBB] SDF format, chain K [auth AAA] SDF format, chain KA [auth BBB] SDF format, chain L [auth AAA] SDF format, chain LA [auth BBB] SDF format, chain M [auth AAA] SDF format, chain MA [auth BBB] SDF format, chain N [auth AAA] SDF format, chain NA [auth BBB] SDF format, chain O [auth AAA] SDF format, chain OA [auth BBB] SDF format, chain P [auth AAA] SDF format, chain Q [auth AAA] SDF format, chain R [auth AAA] SDF format, chain X [auth BBB] SDF format, chain Y [auth BBB] SDF format, chain Z [auth BBB] MOL2 format, chain AA [auth BBB] MOL2 format, chain BA [auth BBB] MOL2 format, chain CA [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain DA [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain EA [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain FA [auth BBB] MOL2 format, chain G [auth AAA] MOL2 format, chain GA [auth BBB] MOL2 format, chain HA [auth BBB] MOL2 format, chain I [auth AAA] MOL2 format, chain IA [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain JA [auth BBB] MOL2 format, chain K [auth AAA] MOL2 format, chain KA [auth BBB] MOL2 format, chain L [auth AAA] MOL2 format, chain LA [auth BBB] MOL2 format, chain M [auth AAA] MOL2 format, chain MA [auth BBB] MOL2 format, chain N [auth AAA] MOL2 format, chain NA [auth BBB] MOL2 format, chain O [auth AAA] MOL2 format, chain OA [auth BBB] MOL2 format, chain P [auth AAA] MOL2 format, chain Q [auth AAA] MOL2 format, chain R [auth AAA] MOL2 format, chain X [auth BBB] MOL2 format, chain Y [auth BBB] MOL2 format, chain Z [auth BBB] mmCIF format, chain AA [auth BBB] mmCIF format, chain BA [auth BBB] mmCIF format, chain CA [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain DA [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain EA [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain FA [auth BBB] mmCIF format, chain G [auth AAA] mmCIF format, chain GA [auth BBB] mmCIF format, chain HA [auth BBB] mmCIF format, chain I [auth AAA] mmCIF format, chain IA [auth BBB] mmCIF format, chain J [auth AAA] mmCIF format, chain JA [auth BBB] mmCIF format, chain K [auth AAA] mmCIF format, chain KA [auth BBB] mmCIF format, chain L [auth AAA] mmCIF format, chain LA [auth BBB] mmCIF format, chain M [auth AAA] mmCIF format, chain MA [auth BBB] mmCIF format, chain N [auth AAA] mmCIF format, chain NA [auth BBB] mmCIF format, chain O [auth AAA] mmCIF format, chain OA [auth BBB] mmCIF format, chain P [auth AAA] mmCIF format, chain Q [auth AAA] mmCIF format, chain R [auth AAA] mmCIF format, chain X [auth BBB] mmCIF format, chain Y [auth BBB] mmCIF format, chain Z [auth BBB]	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		Interactions Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain CA [auth BBB] Focus chain D [auth AAA] Focus chain DA [auth BBB] Focus chain E [auth AAA] Focus chain EA [auth BBB] Focus chain F [auth AAA] Focus chain FA [auth BBB] Focus chain G [auth AAA] Focus chain GA [auth BBB] Focus chain HA [auth BBB] Focus chain I [auth AAA] Focus chain IA [auth BBB] Focus chain J [auth AAA] Focus chain JA [auth BBB] Focus chain K [auth AAA] Focus chain KA [auth BBB] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain N [auth AAA] Focus chain NA [auth BBB] Focus chain O [auth AAA] Focus chain OA [auth BBB] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain X [auth BBB] Focus chain Y [auth BBB] Focus chain Z [auth BBB] Interactions & Density Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain CA [auth BBB] Focus chain D [auth AAA] Focus chain DA [auth BBB] Focus chain E [auth AAA] Focus chain EA [auth BBB] Focus chain F [auth AAA] Focus chain FA [auth BBB] Focus chain G [auth AAA] Focus chain GA [auth BBB] Focus chain HA [auth BBB] Focus chain I [auth AAA] Focus chain IA [auth BBB] Focus chain J [auth AAA] Focus chain JA [auth BBB] Focus chain K [auth AAA] Focus chain KA [auth BBB] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain N [auth AAA] Focus chain NA [auth BBB] Focus chain O [auth AAA] Focus chain OA [auth BBB] Focus chain P [auth AAA] Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain X [auth BBB] Focus chain Y [auth BBB] Focus chain Z [auth BBB]