3VHC

Hsp90 alpha N-terminal domain in complex with a macrocyclic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3VHC/pdb

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


• Deposited: 2011-08-24 Released: 2012-07-18 
• Deposition Author(s): Fukami, T.A., Ono, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.220 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Design and synthesis of novel macrocyclic 2-amino-6-arylpyrimidine Hsp90 inhibitors

Suda, A., Koyano, H., Hayase, T., Hada, K., Kawasaki, K., Komiyama, S., Hasegawa, K., Fukami, T.A., Sato, S., Miura, T., Ono, N., Yamazaki, T., Saitoh, R., Shimma, N., Shiratori, Y., Tsukuda, T.

(2012) Bioorg Med Chem Lett 22: 1136-1141

• PubMed: 22192591 
• DOI: https://doi.org/10.1016/j.bmcl.2011.11.100
• Primary Citation of Related Structures:  
  3VHA, 3VHC, 3VHD


• PubMed Abstract: 
  

  Macrocyclic compounds bearing a 2-amino-6-arylpyrimidine moiety were identified as potent heat shock protein 90 (Hsp90) inhibitors by modification of 2-amino-6-aryltriazine derivative (CH5015765). We employed a macrocyclic structure as a skeleton of new inhibitors to mimic the geldanamycin-Hsp90 interactions. Among the identified inhibitors, CH5164840 showed high binding affinity for N-terminal Hsp90α (K(d)=0.52nM) and strong anti-proliferative activity against human cancer cell lines (HCT116 IC(50)=0.15μM, NCI-N87 IC(50)=0.066μM). CH5164840 displayed high oral bioavailability in mice (F=70.8%) and potent antitumor efficacy in a HCT116 human colorectal cancer xenograft model (tumor growth inhibition=83%).

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Organizational Affiliation: 

Kamakura Laboratories, Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.22 kDa 
• Atom Count: 2,059 
• Modelled Residue Count: 216 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	229	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1 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
VHC	B [auth A]	4-amino-20,22-dimethyl-13-oxa-7-thia-3,5,17-triazatetracyclo[17.3.1.1~2,6~.1~8,12~]pentacosa-1(23),2(25),3,5,8(24),9,11,19,21-nonaen-18-one C22 H22 N4 O2 S HDKDXSZAJVZYLD-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VHC	PDBBind:  3VHC	Kd: 1.3 (nM) from 1 assay(s)
	BindingDB:  3VHC	Kd: 1.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.220 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.795	α = 90
b = 44.004	β = 114.35
c = 53.897	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Fukami, T.A., Ono, N.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations