4O6L | pdb_00004o6l

Crystal Structure of TTK kinase domain with an inhibitor: 401498 (N-[(1R)-1-(2-chlorophenyl)propyl]-3-{4-[(1-methylpiperidin-4-yl)oxy]phenyl}-1H-indazole-5-carboxamide)

• PDB DOI: https://doi.org/10.2210/pdb4O6L/pdb

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


• Deposited: 2013-12-22 Released: 2014-12-24 
• Deposition Author(s): Qiu, W., Plotnikova, O., Feher, M., Awrey, D.E., Chirgadze, N.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal Structure of TTK kinase domain with an inhibitor: 401498

Qiu, W., Plotnikova, O., Feher, M., Awrey, D.E., Chirgadze, N.Y.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.59 kDa 
• Atom Count: 4,375 
• Modeled Residue Count: 516 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase TTK	A, B	281	Homo sapiens	Mutation(s): 0  Gene Names: TTK, MPS1, MPS1L1 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P33981 (Homo sapiens) Explore P33981  Go to UniProtKB:  P33981
PHAROS:  P33981 GTEx:  ENSG00000112742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2QK	C [auth A], E [auth B]	N-[(1R)-1-(2-chlorophenyl)propyl]-3-{4-[(1-methylpiperidin-4-yl)oxy]phenyl}-1H-indazole-5-carboxamide C29 H31 Cl N4 O2 XEADJJXUBNVGAN-AREMUKBSSA-N
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
2QK	BindingDB:  4O6L	IC50: 1.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.232	α = 90
b = 70.26	β = 133.14
c = 106.889	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Qiu, W., Plotnikova, O., Feher, M., Awrey, D.E., Chirgadze, N.Y.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary