2QFO

HSP90 complexed with A143571 and A516383


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.246 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery and design of novel HSP90 inhibitors using multiple fragment-based design strategies.

Huth, J.R.Park, C.Petros, A.M.Kunzer, A.R.Wendt, M.D.Wang, X.Lynch, C.L.Mack, J.C.Swift, K.M.Judge, R.A.Chen, J.Richardson, P.L.Jin, S.Tahir, S.K.Matayoshi, E.D.Dorwin, S.A.Ladror, U.S.Severin, J.M.Walter, K.A.Bartley, D.M.Fesik, S.W.Elmore, S.W.Hajduk, P.J.

(2007) Chem Biol Drug Des 70: 1-12

  • DOI: https://doi.org/10.1111/j.1747-0285.2007.00535.x
  • Primary Citation of Related Structures:  
    2QF6, 2QFO, 2QG0, 2QG2

  • PubMed Abstract: 

    The molecular chaperone HSP90 has been shown to facilitate cancer cell survival by stabilizing key proteins responsible for a malignant phenotype. We report here the results of parallel fragment-based drug design approaches in the design of novel HSP90 inhibitors. Initial aminopyrimidine leads were elaborated using high-throughput organic synthesis to yield nanomolar inhibitors of the enzyme. Second site leads were also identified which bound to HSP90 in two distinct conformations, an 'open' and 'closed' form. Intriguingly, linked fragment approaches targeting both of these conformations were successful in producing novel, micromolar inhibitors. Overall, this study shows that, with only a few fragment hits, multiple lead series can be generated for HSP90 due to the inherent flexibility of the active site. Thus, ample opportunities exist to use these lead series in the development of clinically useful HSP90 inhibitors for the treatment of cancers.


  • Organizational Affiliation

    Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha
A, B
207Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
GTEx:  ENSG00000080824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A51
Query on A51

Download Ideal Coordinates CCD File 
D [auth A](3E)-3-[(phenylamino)methylidene]dihydrofuran-2(3H)-one
C11 H11 N O2
BKXNPYSVWOVZGX-CMDGGOBGSA-N
A13
Query on A13

Download Ideal Coordinates CCD File 
C [auth A]4-METHYL-6-(TRIFLUOROMETHYL)PYRIMIDIN-2-AMINE
C6 H6 F3 N3
CNTCLEOUAMWZGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A13 BindingDB:  2QFO Ki: 1.80e+4 (nM) from 1 assay(s)
Kd: 2.00e+4 (nM) from 1 assay(s)
PDBBind:  2QFO Kd: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.157α = 90
b = 88.755β = 90
c = 98.445γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2008-07-01 
  • Deposition Author(s): Park, C.H.

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-04-16
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description