8A4U

Crystal structure of human cathepsin L with CAA0225

PDB DOI: https://doi.org/10.2210/pdb8A4U/pdb

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

Deposited: 2022-06-13 Released: 2023-07-05
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., 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: 1.90 Å
R-Value Free: 0.209
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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., Chapman, H.N., Hinrichs, W., Turk, D., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 100.22 kDa
Atom Count: 7,337
Modelled Residue Count: 860
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L2X (Subject of Investigation/LOI) Query on L2X Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D]	E [auth A], M [auth B], P [auth C], U [auth D]	(2S,3S)-N3-[2-(4-hydroxyphenyl)ethyl]-N2-[(2S)-1-oxidanylidene-3-phenyl-1-[(phenylmethyl)amino]propan-2-yl]oxirane-2,3-dicarboxamide C₂₈ H₂₉ N₃ O₅ ZMZQYVMNDRBKLO-SDHOMARFSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain U [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain X [auth D] MOL2 format, chain X [auth D]	X [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-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 O [auth B] MOL2 format, chain O [auth B]	O [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], R [auth C], S [auth C], V [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D]	T [auth C], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain T [auth C] Focus chain W [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth C]	F [auth A], G [auth A], Q [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.209
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57	α = 104.044
b = 62.87	β = 95.826
c = 65.18	γ = 116.051

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

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
German Federal Ministry for Education and Research	Germany	16GW0277
Slovenian Research Agency	Slovenia	P1-0048
Slovenian Research Agency	Slovenia	IO-0048