5TE0 | pdb_00005te0

Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with BIBF 1120

• PDB DOI: https://doi.org/10.2210/pdb5TE0/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-20 Released: 2016-11-02 
• Deposition Author(s): Counago, R.M., Elkins, J.M., Bountra, C., Arruda, P., Edwards, A.M., Gileadi, O., Structural Genomics Consortium (SGC)
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with BIBF 1120

Counago, R.M., Elkins, J.M., Arrowsmith, C.H., Bountra, C., Arruda, P., Edwards, A.M., Gileadi, O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.47 kDa 
• Atom Count: 2,830 
• Modeled Residue Count: 316 
• Deposited Residue Count: 347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP2-associated protein kinase 1	A	347	Homo sapiens	Mutation(s): 0  Gene Names: AAK1, KIAA1048 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XIN	B [auth A]	methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate C31 H33 N5 O4 XZXHXSATPCNXJR-ZIADKAODSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XIN	BindingDB:  5TE0	Kd: 63 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.465	α = 90
b = 119.474	β = 90
c = 125.035	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Counago, R.M., Elkins, J.M., Bountra, C., Arruda, P., Edwards, A.M., Gileadi, O., Structural Genomics Consortium (SGC)

---

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/50724-5

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description