4WSQ

Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Family-wide Structural Analysis of Human Numb-Associated Protein Kinases.

Sorrell, F.J.Szklarz, M.Abdul Azeez, K.R.Elkins, J.M.Knapp, S.

(2016) Structure 24: 401-411

  • DOI: https://doi.org/10.1016/j.str.2015.12.015
  • Primary Citation of Related Structures:  
    4W9W, 4W9X, 4WSQ

  • PubMed Abstract: 

    The highly diverse Numb-associated kinase (NAK) family has been linked to broad cellular functions including receptor-mediated endocytosis, Notch pathway modulation, osteoblast differentiation, and dendrite morphogenesis. Consequently, NAK kinases play a key role in a diverse range of diseases from Parkinson's and prostate cancer to HIV. Due to the plasticity of this kinase family, NAK kinases are often inhibited by approved or investigational drugs and have been associated with side effects, but they are also potential drug targets. The presence of cysteine residues in some NAK family members provides the possibility for selective targeting via covalent inhibition. Here we report the first high-resolution structures of kinases AAK1 and BIKE in complex with two drug candidates. The presented data allow a comprehensive structural characterization of the NAK kinase family and provide the basis for rational design of selective NAK inhibitors.


  • Organizational Affiliation

    Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute (TDI), University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP2-associated protein kinase 1
A, B
317Homo sapiensMutation(s): 0 
Gene Names: AAK1KIAA1048
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q2M2I8 (Homo sapiens)
Explore Q2M2I8 
Go to UniProtKB:  Q2M2I8
PHAROS:  Q2M2I8
GTEx:  ENSG00000115977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2M2I8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KSA
Query on KSA

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
K-252A
C27 H21 N3 O5
KOZFSFOOLUUIGY-SOLYNIJKSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.66α = 90
b = 71.32β = 90
c = 183.64γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references
  • Version 1.2: 2016-03-09
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description