3FZK

Crystal Structures of Hsc70/Bag1 in Complex with Small Molecule Inhibitors

PDB DOI: https://doi.org/10.2210/pdb3FZK/pdb

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

Deposited: 2009-01-26 Released: 2009-03-17
Deposition Author(s): Dokurno, P., Williamson, D.S., Murray, J.B., Surgenor, A.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.294
R-Value Work: 0.215
R-Value Observed: 0.222

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Novel adenosine-derived inhibitors of 70 kDa heat shock protein, discovered through structure-based design

Williamson, D.S., Borgognoni, J., Clay, A., Daniels, Z., Dokurno, P., Drysdale, M.J., Foloppe, N., Francis, G.L., Graham, C.J., Howes, R., Macias, A.T., Murray, J.B., Parsons, R., Shaw, T., Surgenor, A.E., Terry, L., Wang, Y., Wood, M., Massey, A.J.

(2009) J Med Chem 52: 1510-1513

PubMed: 19256508 Search on PubMed
DOI: https://doi.org/10.1021/jm801627a
Primary Citation of Related Structures:
3FZF, 3FZH, 3FZK, 3FZL, 3FZM

PubMed Abstract:
The design and synthesis of novel adenosine-derived inhibitors of HSP70, guided by modeling and X-ray crystallographic structures of these compounds in complex with HSC70/BAG-1, is described. Examples exhibited submicromolar affinity for HSP70, were highly selective over HSP90, and some displayed potency against HCT116 cells. Exposure of compound 12 to HCT116 cells caused significant reduction in cellular levels of Raf-1 and Her2 at concentrations similar to that which caused cell growth arrest.

Organizational Affiliation

Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom. d.williamson@vernalis.com

Macromolecule Content

Total Structure Weight: 55.84 kDa
Atom Count: 4,130
Modelled Residue Count: 488
Deposited Residue Count: 495
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock cognate 71 kDa protein	A	381	Homo sapiens	Mutation(s): 0 Gene Names: HSPA8, HSC70, HSP73, HSPA10 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11142 (Homo sapiens) Explore P11142 Go to UniProtKB: P11142
PHAROS: P11142 GTEx: ENSG00000109971
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11142
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BAG family molecular chaperone regulator 1	B	114	Homo sapiens	Mutation(s): 0 Gene Names: BAG1, HAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q99933 (Homo sapiens) Explore Q99933 Go to UniProtKB: Q99933
PHAROS: Q99933 GTEx: ENSG00000107262
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99933
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3BK Query on 3BK 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]	(2R,3R,4S,5R)-2-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol C₁₇ H₁₈ Cl₂ N₆ O₄ VBJKVZXRYLCYGQ-XNIJJKJLSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3BK	BindingDB: 3FZK	Ki: 4310 (nM) from 1 assay(s)
		Kd: min: 3500, max: 3548 (nM) from 2 assay(s)
		IC50: 9100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.294
R-Value Work: 0.215
R-Value Observed: 0.222
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.504	α = 90
b = 119.896	β = 106.52
c = 53.047	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary