7CJA | pdb_00007cja

Crystal structure of TTK kinase domain in complex with compound 28

• PDB DOI: https://doi.org/10.2210/pdb7CJA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-07-09 Released: 2021-05-12 
• Deposition Author(s): Kim, H.L., Cho, H.Y., Park, Y.W., Lee, Y.H., Son, J.B., Ko, E.H., Choi, H.G., Kim, N.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystal Structure-Guided Design and Optimization of 7 H -Pyrrolo[2,3- d ]pyrimidine-5-carbonitrile Scaffold as a Potent and Orally Active Monopolar Spindle 1 Inhibitor.

Lee, Y., Kim, H., Kim, H., Cho, H.Y., Jee, J.G., Seo, K.A., Son, J.B., Ko, E., Choi, H.G., Kim, N.D., Kim, I.

(2021) J Med Chem 64: 6985-6995

• PubMed: 33942608 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c00542
• Primary Citation of Related Structures:  
  7CHM, 7CHN, 7CHT, 7CIL, 7CJA, 7CLH


• PubMed Abstract: 
  

  Triple-negative breast cancer (TNBC) is an aggressive breast-cancer subtype associated with poor prognosis and high relapse rates. Monopolar spindle 1 kinase (MPS1) is an apical dual-specificity protein kinase that is over-expressed in TNBC. We herein report a highly selective MPS1 inhibitor based on a 7 H -pyrrolo[2,3- d ]pyrimidine-5-carbonitrile scaffold. Our lead optimization was guided by key X-ray crystal structure analysis. In vivo evaluation of candidate ( 9 ) is shown to effectively mitigate human TNBC cell proliferation.

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Organizational Affiliation: 

College of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, South Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.47 kDa 
• Atom Count: 2,213 
• Modelled Residue Count: 265 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase TTK	A	283	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G0U (Subject of Investigation/LOI)	B [auth A]	4-(cyclopentylmethylamino)-2-[[2-methoxy-4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]amino]-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile C24 H27 N7 O2 HNTNJDLDWXMVRF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.644	α = 90
b = 110.536	β = 90
c = 112.456	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Kim, H.L., Cho, H.Y., Park, Y.W., Lee, Y.H., Son, J.B., Ko, E.H., Choi, H.G., Kim, N.D.

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2021-06-09
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary