7A5D | pdb_00007a5d

Structure of DYRK1A in complex with compound 16

• PDB DOI: https://doi.org/10.2210/pdb7A5D/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-21 Released: 2021-06-30 
• Deposition Author(s): Dokurno, P., Surgenor, A.E., Hubbard, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.198 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Fragment-Derived Selective Inhibitors of Dual-Specificity Kinases DYRK1A and DYRK1B.

Lee Walmsley, D., Murray, J.B., Dokurno, P., Massey, A.J., Benwell, K., Fiumana, A., Foloppe, N., Ray, S., Smith, J., Surgenor, A.E., Edmonds, T., Demarles, D., Burbridge, M., Cruzalegui, F., Kotschy, A., Hubbard, R.E.

(2021) J Med Chem 64: 8971-8991

• PubMed: 34143631 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c00024
• Primary Citation Related Structures: 
  7A4O, 7A4R, 7A4S, 7A4W, 7A4Z, 7A51, 7A52, 7A53, 7A55, 7A5B, 7A5D, 7A5L, 7A5N


• PubMed Abstract: 
  

  The serine/threonine kinase DYRK1A has been implicated in regulation of a variety of cellular processes associated with cancer progression, including cell cycle control, DNA damage repair, protection from apoptosis, cell differentiation, and metastasis. In addition, elevated-level DYRK1A activity has been associated with increased severity of symptoms in Down's syndrome. A selective inhibitor of DYRK1A could therefore be of therapeutic benefit. We have used fragment and structure-based discovery methods to identify a highly selective, well-tolerated, brain-penetrant DYRK1A inhibitor which showed in vivo activity in a tumor model. The inhibitor provides a useful tool compound for further exploration of the effect of DYRK1A inhibition in models of disease.

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Organizational Affiliation: 
• Vernalis (R&D) Ltd., Granta Park, Cambridge CB21 6GB, U.K.
Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine 78290, France.
Technologie Servier, 27 Rue Eugène Vignat, Orleans 45000, France.
Servier Research Institute of Medicinal Chemistry, Záhony u. 7., Budapest H-1031, Hungary.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.97 kDa 
• Atom Count: 3,026 
• Modeled Residue Count: 331 
• Deposited Residue Count: 359 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A	359	Homo sapiens	Mutation(s): 0  Gene Names: DYRK1A, DYRK, MNB, MNBH EC: 2.7.12.1 (PDB Primary Data), 2.7.11.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens) Explore Q13627  Go to UniProtKB:  Q13627
PHAROS:  Q13627 GTEx:  ENSG00000157540

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QYW (Subject of Investigation/LOI)	D [auth A]	4-azanyl-2-methyl-6-pyridin-3-yl-7~{H}-pyrrolo[2,3-d]pyrimidine-5-carbonitrile C13 H10 N6 AWVFEGNSWDVVKZ-UHFFFAOYSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.198 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.696	α = 90
b = 81.696	β = 90
c = 123.601	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Dokurno, P., Surgenor, A.E., Hubbard, R.E.

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2021-07-21
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary