Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 37.63 kDa 
• Atom Count: 2330 
• Modelled Residue Count: 274 
• Deposited Residue Count: 327 
• Unique protein chains: 1

3LM5

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

• PDB DOI: 10.2210/pdb3LM5/pdb

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


• Deposited: 2010-01-29 Released: 2010-03-16 
• Deposition Author(s): Ugochukwu, E., Soundararajan, M., Rellos, P., Fedorov, O., Phillips, C., Wang, J., Hapka, E., Filippakopoulos, P., Chaikuad, A., Pike, A.C.W., Carpenter, L., Vollmar, M., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

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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 

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

• PubMed: 33215924 
• 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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 17B	A	327	Homo sapiens	Mutation(s): 0  Gene Names: DRAK2, STK17B 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUE	B [auth A]	3,5,7,3',4'-PENTAHYDROXYFLAVONE C15 H10 O7 REFJWTPEDVJJIY-UHFFFAOYSA-N

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 = 83.38	α = 90
b = 83.38	β = 90
c = 115.3	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-29 
• Released Date: 2010-03-16 
Deposition Author(s): Ugochukwu, E., Soundararajan, M., Rellos, P., Fedorov, O., Phillips, C., Wang, J., Hapka, E., Filippakopoulos, P., Chaikuad, A., Pike, A.C.W., Carpenter, L., Vollmar, M., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• 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