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

• PDB DOI: https://doi.org/10.2210/pdb3RLQ/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-20 Released: 2011-06-08 
• Deposition Author(s): 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.

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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 

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

• PubMed: 21612924 
• DOI: https://doi.org/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 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).

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Organizational Affiliation: 

Pfizer Worldwide Research and Development, La Jolla Laboratories, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.93 kDa 
• Atom Count: 3,807 
• Modelled Residue Count: 445 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A, B	226	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3RQ	C [auth A], E [auth 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
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
3RQ	PDBBind:  3RLQ	Ki: 40 (nM) from 1 assay(s)
	BindingDB:  3RLQ	IC50: 1000 (nM) from 1 assay(s)

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 = 45.48	α = 90
b = 79.259	β = 90
c = 118.285	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): 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.

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
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations