8HFV

Crystal structure of CTSL in complex with K777

PDB DOI: https://doi.org/10.2210/pdb8HFV/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-12 Released: 2023-12-13
Deposition Author(s): Wang, H., Shao, M., Sun, L., Yang, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.242
R-Value Work: 0.197
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of CTSL in complex with K777

Wang, H., Shao, M., Sun, L., Yang, H.

To be published.

Macromolecule Content

Total Structure Weight: 102 kDa
Atom Count: 7,575
Modelled Residue Count: 874
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
Procathepsin L	A, B, C, D	220	Homo sapiens	Mutation(s): 0 Gene Names: CTSL
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0IW (Subject of Investigation/LOI) Query on 0IW Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain N [auth A] SDF format, chain RA [auth D] SDF format, chain X [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain X [auth B]	HA [auth C], N [auth A], RA [auth D], X [auth B]	Nalpha-[(4-methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-phenylalaninamide C₃₂ H₄₀ N₄ O₄ S VZSXPUDQSLKVIR-JDXGNMNLSA-N		Interactions Focus chain HA [auth C] Focus chain N [auth A] Focus chain RA [auth D] Focus chain X [auth B] Interactions & Density Focus chain HA [auth C] Focus chain N [auth A] Focus chain RA [auth D] Focus chain X [auth B]
CAC (Subject of Investigation/LOI) Query on CAC Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	FA [auth C] GA [auth C] L [auth A] M [auth A] PA [auth D] FA [auth C], GA [auth C], L [auth A], M [auth A], PA [auth D], QA [auth D], V [auth B], W [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain V [auth B] Focus chain W [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] E [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], LA [auth D], MA [auth D], NA [auth D], O [auth B], OA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000325 (0IW) Query on PRD_000325	HA [auth C], N [auth A], RA [auth D], X [auth B]	MePip-Phe-HphVSPh	Peptide-like / Inhibitor		Interactions Focus chain HA [auth C] Focus chain N [auth A] Focus chain RA [auth D] Focus chain X [auth B] Interactions & Density Focus chain HA [auth C] Focus chain N [auth A] Focus chain RA [auth D] Focus chain X [auth B]