6QLM | pdb_00006qlm

Cathepsin-K in complex with MIV-701

PDB DOI: https://doi.org/10.2210/pdb6QLM/pdb

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

Deposited: 2019-02-01 Released: 2020-02-19
Deposition Author(s): Derbyshire, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.142 (Depositor), 0.129 (DCC)
R-Value Work:
0.101 (Depositor), 0.129 (DCC)
R-Value Observed:
0.103 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Successful development of 3-oxohexahydrofuropyrrole amino acid amides as inhibitors of Cathepsin-K.

Derbyshire, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 48.76 kDa
Atom Count: 4,292
Modeled Residue Count: 432
Deposited Residue Count: 432
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	216	Homo sapiens	Mutation(s): 0 Gene Names: CTSK, CTSO, CTSO2 EC: 3.4.22.38
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HFH (Subject of Investigation/LOI) Query on HFH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide C₂₇ H₃₆ F N₅ O₄ S BJRXVCXTMWVZKF-KVFBUXGHSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MHA Query on MHA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID C₆ H₁₀ N₂ O₅ QZTKDVCDBIDYMD-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.142 (Depositor), 0.129 (DCC)
R-Value Work: 0.101 (Depositor), 0.129 (DCC)
R-Value Observed: 0.103 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.537	α = 74.34
b = 51.855	β = 76.39
c = 57.26	γ = 84.7

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

Derbyshire, D.J.

Revision History (Full details and data files)

Version 1.0: 2020-02-19
Type: Initial release
Version 1.1: 2024-11-20
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary