3LDP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.298 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3P1Click on this verticalbar to view details

This is version 1.2 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

  • 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


Macromolecules
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
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11021
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
3P1 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 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
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
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3P1Click on this verticalbar to view details

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