7ZVF

Crystal structure of human cathepsin L in complex with covalently bound CLIK148

PDB DOI: https://doi.org/10.2210/pdb7ZVF/pdb

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

Deposited: 2022-05-15 Released: 2023-11-29
Deposition Author(s): Falke, S., Lieske, J., Guenther, S., Reinke, P.Y.A., Ewert, W., Loboda, J., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Tsuge, H., Chapman, H.N., Hinrichs, W., Turk, D., Meents, A.
Funding Organization(s): Helmholtz Association, German Federal Ministry for Education and Research, Slovenian Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189
R-Value Work: 0.165
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural elucidation of antiviral cathepsin L inhibitors

Falke, S., Lieske, J., Herrmann, A., Guenther, S., Reinke, P.Y.A., Ewert, W., Loboda, J., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Tsuge, H., Chapman, H.N., Hinrichs, W., Ebert, G., Turk, D., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 100.95 kDa
Atom Count: 7,667
Modelled Residue Count: 880
Deposited Residue Count: 880
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens) Explore P07711 Go to UniProtKB: P07711
PHAROS: P07711 GTEx: ENSG00000135047
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07711
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KXL (Subject of Investigation/LOI) Query on KXL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain E [auth A] SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D]	E [auth A], M [auth B], R [auth C], W [auth D]	(2S)-N-[(2S)-1-(dimethylamino)-1-oxidanylidene-3-phenyl-propan-2-yl]-2-oxidanyl-N'-(2-pyridin-2-ylethyl)butanediamide C₂₂ H₂₈ N₄ O₄ WUIQDGGROZLMJW-OALUTQOASA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain P [auth B] SDF format, chain G [auth A] SDF format, chain T [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth C]	BA [auth D], G [auth A], P [auth B], T [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain P [auth B] Focus chain T [auth C] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain P [auth B] Focus chain T [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain AA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] J [auth A] K [auth A] L [auth A] S [auth C] AA [auth D], J [auth A], K [auth A], L [auth A], S [auth C], X [auth D], Y [auth D], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	CA [auth D] DA [auth D] EA [auth D] H [auth A] I [auth A] CA [auth D], DA [auth D], EA [auth D], H [auth A], I [auth A], N [auth B], O [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C]	U [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth B]	Q [auth B], V [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain Q [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189
R-Value Work: 0.165
R-Value Observed: 0.165
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.22	α = 105.528
b = 62.29	β = 93.561
c = 68.03	γ = 115.725

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	FISCOV
Helmholtz Association	Germany	SFragX
German Federal Ministry for Education and Research	Germany	031B0405
Slovenian Research Agency	Slovenia	P1-0048
Slovenian Research Agency	Slovenia	IO-0048