34CM | pdb_000034cm

Crystal structure of human Cathepsin L in complex with 8-hydroxy-2,6-diazaspiro[3.5]nonan-5-one

PDB DOI: https://doi.org/10.2210/pdb34CM/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella phaffii GS115
Mutation(s): Yes

Deposited: 2026-09-07 Released: 2026-11-11
Deposition Author(s): Falke, S., Meents, A.
Funding Organization(s): Helmholtz Association, German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.168 (Depositor), 0.168 (DCC)
R-Value Observed:
0.170 (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

To Be Published

Falke, S., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 99.09 kDa
Atom Count: 7,684
Modeled Residue Count: 877
Deposited Residue Count: 880
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L	A, B, C, D	220	Homo sapiens	Mutation(s): 1 Gene Names: CTSL, CTSL1 EC: 3.4.22.15
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens) Explore P07711 Go to UniProtKB: P07711
GTEx: ENSG00000135047
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07711
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
A1KPM (Subject of Investigation/LOI) Query on A1KPM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(8~{R})-8-oxidanyl-2,6-diazaspiro[3.5]nonan-5-one C₇ H₁₂ N₂ O₂ IIRVBVCKAVWMPW-RXMQYKEDSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
A1KTO (Subject of Investigation/LOI) Query on A1KTO Download:Ideal Coordinates CCD File SDF format, chain X [auth D] MOL2 format, chain X [auth D] mmCIF format, chain X [auth D]	X [auth D]	(8~{S})-8-oxidanyl-2,6-diazaspiro[3.5]nonan-5-one C₇ H₁₂ N₂ O₂ IIRVBVCKAVWMPW-YFKPBYRVSA-N		Interactions Focus chain X [auth D] Interactions & Density Focus chain X [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain W [auth D] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain W [auth D] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	H [auth A], N [auth B], W [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain W [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain W [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A] L [auth B] M [auth B] O [auth C] P [auth C] G [auth A], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], V [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain S [auth D] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain S [auth D] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], K [auth B], S [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain S [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D]	T [auth D], U [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain T [auth D] Focus chain U [auth D]