5V19

Structure-based drug design of novel ASK1 inhibitors using a fully integrated lead optimization strategy

• PDB DOI: https://doi.org/10.2210/pdb5V19/pdb

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


• Deposited: 2017-03-01 Released: 2017-03-29 
• Deposition Author(s): Dougan, D.R., Lawson, J.D., Lane, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.285 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

Structure-based drug design of novel ASK1 inhibitors using an integrated lead optimization strategy.

Gibson, T.S., Johnson, B., Fanjul, A., Halkowycz, P., Dougan, D.R., Cole, D., Swann, S.

(2017) Bioorg Med Chem Lett 27: 1709-1713

• PubMed: 28291695 
• DOI: https://doi.org/10.1016/j.bmcl.2017.02.079
• Primary Citation of Related Structures:  
  5V19, 5V24


• PubMed Abstract: 
  

  Structure-based drug design is an iterative process that is an established means to accelerate lead optimization, and is most powerful when integrated with information from different sources. Herein is described the use of such methods in conjunction with deconstruction and re-optimization of a diverse series of ASK1 chemotypes along with high-throughput screening that lead to the identification of a novel series of efficient ASK1 inhibitors displaying robust MAP3K pathway inhibition.

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Organizational Affiliation: 

Medicinal Chemistry Gastrointestinal Drug Discovery Unit, Takeda California Inc., 10410 Science Center Drive, San Diego, CA 92121, United States. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.43 kDa 
• Atom Count: 4,088 
• Modelled Residue Count: 510 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 5	A, B	271	Homo sapiens	Mutation(s): 0  Gene Names: MAP3K5, ASK1, MAPKKK5, MEKK5 EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q99683 (Homo sapiens) Explore Q99683  Go to UniProtKB:  Q99683
PHAROS:  Q99683 GTEx:  ENSG00000197442

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8V4	C [auth A], D [auth B]	N-(1-ethyl-1H-pyrazol-4-yl)furan-3-carboxamide C10 H11 N3 O2 ILHOJKHFOLVBOJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.285 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.595	α = 90
b = 78.595	β = 90
c = 433.472	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Dougan, D.R., Lawson, J.D., Lane, W.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references