1UYC | pdb_00001uyc

Human Hsp90-alpha with 9-Butyl-8-(2,5-dimethoxy-benzyl)-9H-purin-6-ylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure-Activity Relationships in Purine-Based Inhibitor Binding to Hsp90 Isoforms

Wright, L.Barril, X.Dymock, B.Sheridan, L.Surgenor, A.Beswick, M.Drysdale, M.Collier, A.Massey, A.Davies, N.Fink, A.Fromont, C.Aherne, W.Boxall, K.Sharp, S.Workman, P.Hubbard, R.E.

(2004) Chem Biol 11: 775

  • DOI: https://doi.org/10.1016/j.chembiol.2004.03.033
  • Primary Citation Related Structures: 
    1UY6, 1UY7, 1UY8, 1UY9, 1UYC, 1UYD, 1UYE, 1UYF, 1UYG, 1UYH, 1UYI, 1UYK, 1UYL, 1UYM

  • PubMed Abstract: 

    Inhibition of the ATPase activity of the chaperone protein HSP90 is a potential strategy for treatment of cancers. We have determined structures of the HSP90alpha N-terminal domain complexed with the purine-based inhibitor, PU3, and analogs with enhanced potency both in enzyme and cell-based assays. The compounds induce upregulation of HSP70 and downregulation of the known HSP90 client proteins Raf-1, CDK4, and ErbB2, confirming that the molecules inhibit cell growth by a mechanism dependent on HSP90 inhibition. We have also determined the first structure of the N-terminal domain of HSP90beta, complexed with PU3. The structures allow a detailed rationale to be developed for the observed affinity of the PU3 class of compounds for HSP90 and also provide a structural framework for design of compounds with improved binding affinity and drug-like properties.


  • Organizational Affiliation
    • Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge CB1 6GB, UK.

Macromolecule Content 

  • Total Structure Weight: 26.94 kDa 
  • Atom Count: 1,938 
  • Modeled Residue Count: 209 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HEAT SHOCK PROTEIN HSP 90-ALPHA236Homo sapiensMutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PU7

Query on PU7



Download:Ideal Coordinates CCD File
B [auth A]9-BUTYL-8-(2,5-DIMETHOXY-BENZYL)-9H-PURIN-6-YLAMINE
C18 H23 N5 O2
PPFZLLAIQRZNJE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PU7 BindingDB:  1UYC IC50: 4.10e+4 (nM) from 1 assay(s)
EC50: 1.20e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.778α = 90
b = 90.966β = 90
c = 98.888γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-01
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description