3M3Z

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Heat shock cognate 71 kDa protein381Homo sapiensMutation(s): 0 
Gene Names: HSPA8HSC70HSP73HSPA10
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11142
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BAG family molecular chaperone regulator 1114Homo sapiensMutation(s): 0 
Gene Names: BAG1HAP
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99933
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3F5
Query on 3F5

Download Ideal Coordinates CCD File 
C [auth A]5'-O-(2-amino-2-oxoethyl)-8-(methylamino)adenosine
C13 H19 N7 O5
YTEPWBADDXGTBX-JJNLEZRASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3F5 PDBBind:  3M3Z Ki: 1850 (nM) from 1 assay(s)
BindingDB:  3M3Z Ki: 1850 (nM) from 1 assay(s)
Binding MOAD:  3M3Z Kd: 1.24e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.776α = 90
b = 120.969β = 106.78
c = 53.537γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata 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: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description