9G6A | pdb_00009g6a

Peptide-Small Molecule Hybrids as Novel Selective Irreversible Cathepsin-K Inhibitors in Primary Osteoclasts and Human Lung Cancer Tissue

PDB DOI: https://doi.org/10.2210/pdb9G6A/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella phaffii
Mutation(s): No

Deposited: 2024-07-18 Released: 2025-07-30
Deposition Author(s): Turk, D., Loboda, J.
Funding Organization(s): Israel Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.206 (Depositor), 0.179 (DCC)
R-Value Work:
0.180 (Depositor), 0.181 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Peptide-Small Molecule Hybrids as Novel Selective Irreversible Cathepsin-K Inhibitors in Primary Osteoclasts and Human Lung Cancer Tissue

Gourag, D., Loboda, J.

To be published.

Macromolecule Content

Total Structure Weight: 48.8 kDa
Atom Count: 3,822
Modeled Residue Count: 431
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A, B	216	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43235
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IJC (Subject of Investigation/LOI) Query on A1IJC Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	(2~{S})-4-methyl-~{N}-(2-oxidanylidenepropyl)-2-[[(1~{S})-2,2,2-tris(fluoranyl)-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide C₂₄ H₂₉ F₃ N₂ O₄ S NZWQSEGBYPEJET-VXKWHMMOSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], K [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]