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.

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)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33981
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2QK Query on 2QK Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

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

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Chirgadze, N.Y.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.