3RLQ

Co-crystal structure of the HSP90 ATP binding domain in complex with 4-(2,4-dichloro-5-methoxyphenyl)-2-methyl-7H-pyrrolo[2,3-d]pyrimidine-5- carbonitrile

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Design strategies to target crystallographic waters applied to the Hsp90 molecular chaperone.

Kung, P.P., Sinnema, P.J., Richardson, P., Hickey, M.J., Gajiwala, K.S., Wang, F., Huang, B., McClellan, G., Wang, J., Maegley, K., Bergqvist, S., Mehta, P.P., Kania, R.

(2011) Bioorg Med Chem Lett 21: 3557-3562

  • DOI: 10.1016/j.bmcl.2011.04.130
  • Primary Citation of Related Structures:  
    3RLP, 3RLQ, 3RLR

  • PubMed Abstract: 

    • A series of novel and potent small molecule Hsp90 inhibitors was optimized using X-ray crystal structures. These compounds bind in a deep pocket of the Hsp90 enzyme that is partially comprised by residues Asn51 and Ser52. Displacement of several water mo ...

    A series of novel and potent small molecule Hsp90 inhibitors was optimized using X-ray crystal structures. These compounds bind in a deep pocket of the Hsp90 enzyme that is partially comprised by residues Asn51 and Ser52. Displacement of several water molecules observed crystallographically in this pocket using rule-based strategies led to significant improvements in inhibitor potency. An optimized inhibitor (compound 17) exhibited potent Hsp90 inhibition in ITC, biochemical, and cell-based assays (K(d)=1.3 nM, K(i)=15 nM, and cellular IC(50)=0.5 μM).

    Organizational Affiliation: 

    Pfizer Worldwide Research and Development, La Jolla Laboratories, San Diego, CA 92121, USA. peipei.kung@pfizer.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha A, B226Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
NIH Common Fund Data Resources
PHAROS:  P07900
GTEx:  ENSG00000080824
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3RQ
Query on 3RQ
Download Ideal Coordinates CCD File 
A, B
4-(2,4-dichloro-5-methoxyphenyl)-2-methyl-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
C15 H10 Cl2 N4 O
XQAFNWQVIXKAPE-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3RQKi:  40   nM  Binding MOAD
3RQKi :  40   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.48α = 90
b = 79.259β = 90
c = 118.285γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary