3LDP

Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LDP/pdb

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


• Deposited: 2010-01-13 Released: 2011-01-26 
• Deposition Author(s): Dokurno, P., Surgenor, A.E., Shaw, T., Macias, A.T., Massey, A.J., Williamson, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.298 
• R-Value Work: 0.206 
• R-Value Observed: 0.213 

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 
• DOI: https://doi.org/10.1021/jm101625x
• Primary Citation of 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.

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Organizational Affiliation: 

Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, CB21 6GB, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.45 kDa 
• Atom Count: 6,207 
• Modelled Residue Count: 762 
• Deposited Residue Count: 768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
78 kDa glucose-regulated protein	A, B	384	Homo sapiens	Mutation(s): 0  Gene Names: HSPA5, GRP78 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11021 (Homo sapiens) Explore P11021  Go to UniProtKB:  P11021
PHAROS:  P11021 GTEx:  ENSG00000044574

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3P1	C [auth A], D [auth B]	8-[(quinolin-2-ylmethyl)amino]adenosine C20 H21 N7 O4 NAHSCHKAPXMNFP-NVQRDWNXSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3P1	PDBBind:  3LDP	Kd: 2410 (nM) from 1 assay(s)
	BindingDB:  3LDP	Kd: 2410 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.298 
• R-Value Work: 0.206 
• R-Value Observed: 0.213 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.243	α = 90
b = 74.621	β = 99.8
c = 89.502	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations