5QCH | pdb_00005qch

Crystal structure of human Cathepsin-S with bound ligand

PDB DOI: https://doi.org/10.2210/pdb5QCH/pdb
Deposition Group: G_1002040 ExploreG_1002040

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2017-08-04 Released: 2017-12-20
Deposition Author(s): Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.251 (Depositor), 0.270 (DCC)
R-Value Work:
0.199 (Depositor), 0.220 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

Crystal structure of human Cathepsin-S with bound ligand

Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

To be published.

Macromolecule Content

Total Structure Weight: 101.43 kDa
Atom Count: 8,240
Modelled Residue Count: 891
Deposited Residue Count: 892
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B, C, D	223	Homo sapiens	Mutation(s): 1 Gene Names: CTSS EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens) Explore P25774 Go to UniProtKB: P25774
PHAROS: P25774 GTEx: ENSG00000163131
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25774
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BJS Query on BJS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	F [auth A], I [auth B], K [auth C], N [auth D]	2-(3-[3-({3-[(benzylamino)methyl]-4-chlorophenyl}ethynyl)-4-chlorophenyl]-1-{3-[(3S)-3-methylmorpholin-4-yl]propyl}-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl)-2-oxoacetamide C₃₈ H₄₀ Cl₂ N₆ O₃ CIONECARUUEYBQ-SANMLTNESA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain M [auth D] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D]	H [auth B], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain M [auth D] Interactions & Density Focus chain H [auth B] Focus chain M [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
BJS	BindingDB: 5QCH	IC50: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.251 (Depositor), 0.270 (DCC)
R-Value Work: 0.199 (Depositor), 0.220 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.12	α = 88.06
b = 68.13	β = 87.69
c = 79.02	γ = 73.08

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2018-02-21
Changes: Structure summary
Version 2.0: 2018-06-06
Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
Version 2.1: 2021-02-10
Changes: Database references, Structure summary
Version 2.2: 2021-11-17
Changes: Advisory, Database references, Structure summary
Version 2.3: 2024-11-20
Changes: Data collection, Structure summary

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Help and Resources

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Crystal structure of human Cathepsin-S with bound ligand

Crystal structure of human Cathepsin-S with bound ligand

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

5QCH | pdb_00005qch