6RAA | pdb_00006raa

CLK1 Kinase domain with bound imidazopyridin inhibitor TP003

• PDB DOI: https://doi.org/10.2210/pdb6RAA/pdb

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


• Deposited: 2019-04-05 Released: 2019-04-24 
• Deposition Author(s): Schroeder, M., Arrowsmith, C., Knapp, S., Bountra, C., Edwards, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

CLK1 Kinase domain with bound imidazopyridin inhibitor TP003

Schroeder, M., Arrowsmith, C., Knapp, S., Bountra, C., Edwards, A.

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: 40.13 kDa 
• Atom Count: 3,016 
• Modeled Residue Count: 335 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK1	A	339	Homo sapiens	Mutation(s): 0  Gene Names: CLK1, CLK EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49759 (Homo sapiens) Explore P49759  Go to UniProtKB:  P49759
PHAROS:  P49759 GTEx:  ENSG00000013441

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JWN	B [auth A]	4-[2-methyl-1-(4-methylpiperazin-1-yl)-1-oxidanylidene-propan-2-yl]-~{N}-(6-pyridin-4-ylimidazo[1,2-a]pyridin-2-yl)benzamide C28 H30 N6 O2 IEFFSHLHNYVSEF-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JWN	BindingDB:  6RAA	IC50: 0.67 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.01	α = 90
b = 64.102	β = 117.64
c = 72.383	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Schroeder, M., Arrowsmith, C., Knapp, S., Bountra, C., Edwards, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description