3M3Z | pdb_00003m3z

Crystal structure of HSC70/BAG1 in complex with small molecule inhibitor

PDB DOI: https://doi.org/10.2210/pdb3M3Z/pdb

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

Deposited: 2010-03-10 Released: 2011-01-26
Deposition Author(s): Dokurno, P., Surgenor, A.E., Shaw, T., Macias, A.T., Massey, A.J., Williamson, D.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.293 (Depositor), 0.285 (DCC)
R-Value Work:
0.198 (Depositor), 0.197 (DCC)
R-Value Observed:
0.205 (Depositor)

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

Adenosine-Derived Inhibitors of 78 kDa Glucose Regulated Protein (Grp78) ATPase: Insights into Isoform Selectivity.

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

(2011) J Med Chem 54: 4034-4041

PubMed: 21526763 Search on PubMed
DOI: https://doi.org/10.1021/jm101625x
Primary Citation Related Structures:
3LDL, 3LDN, 3LDO, 3LDP, 3LDQ, 3M3Z

PubMed Abstract:
78 kDa glucose-regulated protein (Grp78) is a heat shock protein (HSP) involved in protein folding that plays a role in cancer cell proliferation. Binding of adenosine-derived inhibitors to Grp78 was characterized by surface plasmon resonance and isothermal titration calorimetry. The most potent compounds were 13 (VER-155008) with K(D) = 80 nM and 14 with K(D) = 60 nM. X-ray crystal structures of Grp78 bound to ATP, ADPnP, and adenosine derivative 10 revealed differences in the binding site between Grp78 and homologous proteins.

Organizational Affiliation

Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, CB21 6GB, UK. a.macias@vernalis.com

Macromolecule Content

Total Structure Weight: 55.6 kDa
Atom Count: 4,185
Modeled Residue Count: 488
Deposited Residue Count: 495
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11142
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99933
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3F5 Query on 3F5 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]	5'-O-(2-amino-2-oxoethyl)-8-(methylamino)adenosine C₁₃ H₁₉ N₇ O₅ YTEPWBADDXGTBX-JJNLEZRASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.293 (Depositor), 0.285 (DCC)
R-Value Work: 0.198 (Depositor), 0.197 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.776	α = 90
b = 120.969	β = 106.78
c = 53.537	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

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Entry History

Deposition Data

Released Date: 2011-01-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary