6S14

Crystal Structure of DYRK1A with small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6S14/pdb

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


• Deposited: 2019-06-18 Released: 2019-06-26 
• Deposition Author(s): Sorrell, F.J., Henderson, S.H., Redondo, C., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Elkins, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.163 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

Kinase Scaffold Repurposing in the Public Domain

Sorrell, F.J., Henderson, S.H., Elkins, J.M., Ward, S.

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 42.92 kDa 
• Atom Count: 3,370 
• Modelled Residue Count: 340 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A	361	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
KQW (Subject of Investigation/LOI)	H [auth A]	~{N}-cyclopropyl-~{N}-methyl-4-pyrazolo[1,5-b]pyridazin-3-yl-pyrimidin-2-amine C14 H14 N6 OAIXSJCARVACKE-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
KQW	BindingDB:  6S14	Kd: 90 (nM) from 1 assay(s)
		IC50: 115 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.163 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.47	α = 90
b = 70.3	β = 118.04
c = 68.53	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Sorrell, F.J., Henderson, S.H., Redondo, C., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Elkins, J.M.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary