6S1J

Crystal Structure of DYRK1A with small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6S1J/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: 1.41 Å
• R-Value Free: 0.176 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

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: 43.2 kDa 
• Atom Count: 3,172 
• Modelled Residue Count: 341 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KRK (Subject of Investigation/LOI)	B [auth A]	3-[2-[(3~{S})-3-fluoranylpyrrolidin-1-yl]pyrimidin-4-yl]pyrazolo[1,5-b]pyridazine C14 H13 F N6 CTKSUQYBSSCMMB-JTQLQIEISA-N
SO4	J [auth A], K [auth A], L [auth A], M [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.176 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.202	α = 90
b = 69.671	β = 117.54
c = 67.44	γ = 90

Software Package:

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

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: 2024-10-16
  Changes: Structure summary