5V19 | pdb_00005v19

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5V19

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1016/j.bmcl.2017.02.079
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Medicinal Chemistry Gastrointestinal Drug Discovery Unit, Takeda California Inc., 10410 Science Center Drive, San Diego, CA 92121, United States. Electronic address: tony.gibson@takeda.com.

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 5
A, B
271Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99683
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.595α = 90
b = 78.595β = 90
c = 433.472γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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