2HH5

Crystal Structure of Cathepsin S in complex with a Zinc mediated non-covalent arylaminoethyl amide

PDB DOI: https://doi.org/10.2210/pdb2HH5/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2006-06-27 Released: 2006-08-15
Deposition Author(s): Spraggon, G., Hornsby, M., Lesley, S.A., Tully, D.C., Harris, J.L., Karenewsky, D.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.220
R-Value Work: 0.173
R-Value Observed: 0.176

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Synthesis and SAR of arylaminoethyl amides as noncovalent inhibitors of cathepsin S: P3 cyclic ethers.

Tully, D.C., Liu, H., Chatterjee, A.K., Alper, P.B., Epple, R., Williams, J.A., Roberts, M.J., Woodmansee, D.H., Masick, B.T., Tumanut, C., Li, J., Spraggon, G., Hornsby, M., Chang, J., Tuntland, T., Hollenbeck, T., Gordon, P., Harris, J.L., Karanewsky, D.S.

(2006) Bioorg Med Chem Lett 16: 5112-5117

PubMed: 16876402 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.07.033
Primary Citation of Related Structures:
2HH5, 2HHN

PubMed Abstract:
The synthesis and structure-activity relationship of a series of arylaminoethyl amide cathepsin S inhibitors are reported. Optimization of P3 and P2 groups to improve overall physicochemical properties resulted in significant improvements in oral bioavailability over early lead compounds. An X-ray structure of compound 37 bound to the active site of cathepsin S is also reported.

Organizational Affiliation

Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, CA 92121, USA. dtully@gnf.org

Macromolecule Content

Total Structure Weight: 50.39 kDa
Atom Count: 3,757
Modelled Residue Count: 434
Deposited Residue Count: 440
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 [auth B], B [auth A]	220	Homo sapiens	Mutation(s): 0 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNQ Query on GNQ Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain L [auth A] MOL2 format, chain G [auth B] MOL2 format, chain L [auth A] mmCIF format, chain G [auth B] mmCIF format, chain L [auth A]	G [auth B], L [auth A]	N-[(1R)-1-[(BENZYLSULFONYL)METHYL]-2-{[(1S)-1-METHYL-2-{[4-(TRIFLUOROMETHOXY)PHENYL]AMINO}ETHYL]AMINO}-2-OXOETHYL]MORPHOLINE-4-CARBOXAMIDE C₂₅ H₃₁ F₃ N₄ O₆ S LIOLGHUQUQDMDF-AVRDEDQJSA-N		Interactions Focus chain G [auth B] Focus chain L [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	C [auth B] D [auth B] E [auth B] H [auth A] I [auth A] C [auth B], D [auth B], E [auth B], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain K [auth A] MOL2 format, chain F [auth B] MOL2 format, chain K [auth A] mmCIF format, chain F [auth B] mmCIF format, chain K [auth A]	F [auth B], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Focus chain K [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
GNQ	BindingDB: 2HH5	Ki: 32 (nM) from 1 assay(s)
GNQ	PDBBind: 2HH5	Ki: 32 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.220
R-Value Work: 0.173
R-Value Observed: 0.176
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.542	α = 90
b = 109.542	β = 90
c = 98.529	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PROCESS	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-08-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary