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

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.213 

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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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
78 kDa glucose-regulated protein
A, B
384Homo sapiensMutation(s): 0 
Gene Names: HSPA5GRP78
UniProt & NIH Common Fund Data Resources
Find proteins for P11021 (Homo sapiens)
Explore P11021 
Go to UniProtKB:  P11021
PHAROS:  P11021
GTEx:  ENSG00000044574 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11021
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3P1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H21 N7 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
3P1 Binding MOAD:  3LDP Kd: 2410 (nM) from 1 assay(s)
PDBBind:  3LDP Kd: 2410 (nM) from 1 assay(s)
BindingDB:  3LDP Kd: 2410 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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 = 56.243α = 90
b = 74.621β = 99.8
c = 89.502γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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: 2024-02-21
    Changes: Data collection, Database references, Derived calculations