1TU6 | pdb_00001tu6

Cathepsin K complexed with a ketoamide inhibitor

PDB DOI: https://doi.org/10.2210/pdb1TU6/pdb

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

Deposited: 2004-06-24 Released: 2004-09-21
Deposition Author(s): Barrett, D.G., Catalano, J.G., Deaton, D.N., Hassell, A.M., Long, S.T., Miller, A.B., Miller, L.R., Shewchuk, L.M., Wells-Knecht, K.J., Wright, L.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.214 (Depositor)
R-Value Work:
0.190 (Depositor)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Potent and selective P2-P3 ketoamide inhibitors of cathepsin K with improved pharmacokinetic properties via favorable P1', P1, and/or P3 substitutions

Barrett, D.G., Catalano, J.G., Deaton, D.N., Hassell, A.M., Long, S.T., Miller, A.B., Miller, L.R., Shewchuk, L.M., Wells-Knecht, K.J., Willard, D.H., Wright, L.L.

(2004) Bioorg Med Chem Lett 14: 4897-4902

PubMed: 15341947 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2004.07.031
Primary Citation Related Structures:
1TU6

PubMed Abstract:
A series of ketoamides were synthesized and evaluated for inhibitory activity against cathepsin K. Exploration of the interactions between achiral P(2) substituents and the cysteine protease based on molecular modelling suggestions resulted in potent cathepsin K inhibitors that demonstrated high selectivity versus cathepsins B, H, and L. Subsequent modifications of the P(3), P(1), and P(1') moieties afforded orally bioavailable inhibitors.

Organizational Affiliation

Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.

Macromolecule Content

Total Structure Weight: 48.22 kDa
Atom Count: 3,751
Modeled Residue Count: 430
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin K	A, B	215	Homo sapiens	Mutation(s): 0 Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38	👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens) Explore P43235 Go to UniProtKB: P43235
PHAROS: P43235 GTEx: ENSG00000143387
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43235
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FSP Query on FSP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	[1-(4-FLUOROBENZYL)CYCLOBUTYL]METHYL (1S)-1-[OXO(1H-PYRAZOL-5-YLAMINO)ACETYL]PENTYLCARBAMATE C₂₃ H₂₉ F N₄ O₄ QTPYRNAKLBXKNP-SFHVURJKSA-N	👁 Image	Focus chain E [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L	👁 Image	Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.214 (Depositor)
R-Value Work: 0.190 (Depositor)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.179	α = 90
b = 66.776	β = 90
c = 107.708	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-09-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary