6HK6

Human RIOK2 bound to inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human RIOK2 bound to a specific inhibitor.

Wang, J.Varin, T.Vieth, M.Elkins, J.M.

(2019) Open Biol 9: 190037-190037

  • DOI: 10.1098/rsob.190037
  • Primary Citation of Related Structures:  
    6HK6

  • PubMed Abstract: 
  • The RIO kinases (RIOKs) are a universal family of atypical kinases that are essential for assembly of the pre-40S ribosome complex. Here, we present the crystal structure of human RIO kinase 2 (RIOK2) bound to a specific inhibitor. This first crystal structure of an inhibitor-bound RIO kinase reveals the binding mode of the inhibitor and explains the structure-activity relationship of the inhibitor series ...

    The RIO kinases (RIOKs) are a universal family of atypical kinases that are essential for assembly of the pre-40S ribosome complex. Here, we present the crystal structure of human RIO kinase 2 (RIOK2) bound to a specific inhibitor. This first crystal structure of an inhibitor-bound RIO kinase reveals the binding mode of the inhibitor and explains the structure-activity relationship of the inhibitor series. The inhibitor binds in the ATP-binding site and forms extensive hydrophobic interactions with residues at the entrance to the ATP-binding site. Analysis of the conservation of active site residues reveals the reasons for the specificity of the inhibitor for RIOK2 over RIOK1 and RIOK3, and it provides a template for inhibitor design against the human RIOK family.


    Organizational Affiliation

    4 Structural Genomics Consortium, Universidade Estadual de Campinas , Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello 550, Barão Geraldo, Campinas/SP 13083-886 , Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase RIO2
A, B, C, D, E, F, G, H, I, J
A, B, C, D, E, F, G, H, I, J
330Homo sapiensMutation(s): 0 
Gene Names: RIOK2RIO2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVS4 (Homo sapiens)
Explore Q9BVS4 
Go to UniProtKB:  Q9BVS4
PHAROS:  Q9BVS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVS4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G8H
Query on G8H

Download Ideal Coordinates CCD File 
BA [auth F],
DA [auth G],
EA [auth H],
HA [auth I],
IA [auth J],
BA [auth F],
DA [auth G],
EA [auth H],
HA [auth I],
IA [auth J],
K [auth A],
Q [auth B],
V [auth C],
X [auth D],
Z [auth E]
2-naphthalen-2-yl-~{N}-pyridin-2-yl-ethanamide
C17 H14 N2 O
KXZCFXKLOSDNKK-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
AA [auth E],
FA [auth H],
R [auth B],
Y [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth F],
N [auth A],
O [auth A],
P [auth A],
S [auth B],
CA [auth F],
N [auth A],
O [auth A],
P [auth A],
S [auth B],
T [auth B],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth H],
L [auth A],
M [auth A],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.01α = 90
b = 92.86β = 99.1
c = 237.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-02
    Changes: Data collection, Derived calculations