Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 27.02 kDa 
• Atom Count: 1780 
• Residue Count: 203 
• Unique protein chains: 1

6EYA

Estimation of relative drug-target residence times by random acceleration molecular dynamics simulation

• DOI: 10.2210/pdb6EYA/pdb

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


• Deposited: 2017-11-11 Released: 2018-05-30 
• Deposition Author(s): Musil, D., Lehmann, M., Buchstaller, H.-P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Estimation of Drug-Target Residence Times by tau-Random Acceleration Molecular Dynamics Simulations.

Kokh, D.B., Amaral, M., Bomke, J., Gradler, U., Musil, D., Buchstaller, H.P., Dreyer, M.K., Frech, M., Lowinski, M., Vallee, F., Bianciotto, M., Rak, A., Wade, R.C.

(2018) J Chem Theory Comput 14: 3859-3869

• PubMed: 29768913 
• DOI: 10.1021/acs.jctc.8b00230
• Primary Citation of Related Structures:  
  5LO5, 5LO6, 6F1N, 6EYB, 6EYA, 6EY9, 6EY8, 6EI5, 6EL5, 6ELN


• PubMed Abstract: 
  

Drug-target residence time (τ), one of the main determinants of drug efficacy, remains highly challenging to predict computationally and, therefore, is usually not considered in the early stages of drug design. Here, we present an efficient computational method, τ-random acceleration molecular dynamics (τRAMD), for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanisms. We assessed τRAMD on a data set of 70 diverse drug-like ligands of the N-terminal domain of HSP90α, a pharmaceutically important target with a highly flexible binding site, obtaining computed relative residence times with an accuracy of about 2.3τ for 78% of the compounds and less than 2.0τ within congeneric series. Analysis of dissociation trajectories reveals features that affect ligand unbinding rates, including transient polar interactions and steric hindrance. These results suggest that τRAMD will be widely applicable as a computationally efficient aid to improving drug residence times during lead optimization.

---

Organizational Affiliation: 

Interdisciplinary Center for Scientific Computing (IWR) , Heidelberg University , Heidelberg 69120 , Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	236	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C4K	A	~{N}-(1,3-benzodioxol-5-yl)-~{N}-methyl-3-[(3-methylphenyl)methyl]-6-oxidanyl-1~{H}-indazole-5-carboxamide C24 H21 N3 O4 YXZVBNOPBJFEOP-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
C4K	Kd:  33   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.989	α = 90
b = 90.769	β = 90
c = 99.494	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-11-11 
• Released Date: 2018-05-30 
Deposition Author(s): Musil, D., Lehmann, M., Buchstaller, H.-P.

Revision History 

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection, Database references