3LM5

Crystal Structure of human Serine/Threonine Kinase 17B (STK17B) in complex with Quercetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.

Picado, A.Chaikuad, A.Wells, C.I.Shrestha, S.Zuercher, W.J.Pickett, J.E.Kwarcinski, F.E.Sinha, P.de Silva, C.S.Zutshi, R.Liu, S.Kannan, N.Knapp, S.Drewry, D.H.Willson, T.M.

(2020) J Med Chem 63: 14626-14646

  • DOI: 10.1021/acs.jmedchem.0c01174
  • Primary Citation of Related Structures:  
    3LM5, 6Y6F, 6Y6H, 6ZJF, 7AKG

  • PubMed Abstract: 
  • STK17B is a member of the death-associated protein kinase family and has been genetically linked to the development of diverse diseases. However, the role of STK17B in normal and disease pathology is poorly defined. Here, we present the discovery of thieno[3,2-d] pyrimidine SGC-STK17B-1 ( 11s ), a high-quality chemical probe for this understudied "dark" kinase ...

    STK17B is a member of the death-associated protein kinase family and has been genetically linked to the development of diverse diseases. However, the role of STK17B in normal and disease pathology is poorly defined. Here, we present the discovery of thieno[3,2-d] pyrimidine SGC-STK17B-1 ( 11s ), a high-quality chemical probe for this understudied "dark" kinase. 11s is an ATP-competitive inhibitor that showed remarkable selectivity over other kinases including the closely related STK17A. X-ray crystallography of 11s and related thieno[3,2-d]pyrimidines bound to STK17B revealed a unique P-loop conformation characterized by a salt bridge between R41 and the carboxylic acid of the inhibitor. Molecular dynamic simulations of STK17B revealed the flexibility of the P-loop and a wide range of R41 conformations available to the apo-protein. The isomeric thieno[2,3-d]pyrimidine SGC-STK17B-1N ( 19g ) was identified as a negative control compound. The >100-fold lower activity of 19g on STK17B was attributed to the reduced basicity of its pyrimidine N1.


    Organizational Affiliation

    Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7264, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 17BA327Homo sapiensMutation(s): 0 
Gene Names: DRAK2STK17B
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O94768 (Homo sapiens)
Explore O94768 
Go to UniProtKB:  O94768
PHAROS:  O94768
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94768
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUE
Query on QUE

Download Ideal Coordinates CCD File 
B [auth A]3,5,7,3',4'-PENTAHYDROXYFLAVONE
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.38α = 90
b = 83.38β = 90
c = 115.3γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-01-13
    Changes: Database references, Derived calculations