6YYP | pdb_00006yyp

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 (Depositor), 0.194 (DCC)
R-Value Work:
0.141 (Depositor), 0.152 (DCC)

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

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: 51.21 kDa
Atom Count: 3,993
Modeled Residue Count: 442
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q1H (Subject of Investigation/LOI) Query on Q1H Download:Ideal Coordinates CCD File SDF format, chain E [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA]	1-(furan-2-ylmethyl)-5-(trifluoromethyl)benzimidazol-2-amine C₁₃ H₁₀ F₃ N₃ O QYVPLFHAOLRMBY-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Interactions & Density Focus chain E [auth AAA]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain F [auth BBB] MOL2 format, chain F [auth BBB] mmCIF format, chain F [auth BBB]	F [auth BBB]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain F [auth BBB] Interactions & Density Focus chain F [auth BBB]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain G [auth BBB] SDF format, chain H [auth BBB] MOL2 format, chain G [auth BBB] MOL2 format, chain H [auth BBB] mmCIF format, chain G [auth BBB] mmCIF format, chain H [auth BBB]	G [auth BBB], H [auth BBB]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain G [auth BBB] Focus chain H [auth BBB] Interactions & Density Focus chain G [auth BBB] Focus chain H [auth BBB]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain I [auth BBB] SDF format, chain J [auth BBB] SDF format, chain K [auth BBB] SDF format, chain L [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain I [auth BBB] MOL2 format, chain J [auth BBB] MOL2 format, chain K [auth BBB] MOL2 format, chain L [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain I [auth BBB] mmCIF format, chain J [auth BBB] mmCIF format, chain K [auth BBB] mmCIF format, chain L [auth BBB]	C [auth AAA] D [auth AAA] I [auth BBB] J [auth BBB] K [auth BBB] 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		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain I [auth BBB] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain L [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain I [auth BBB] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain L [auth BBB]