4NCT

Human DYRK1A in complex with PKC412


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.597 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine.

Alexeeva, M.Aberg, E.Engh, R.A.Rothweiler, U.

(2015) Acta Crystallogr.,Sect.D 71: 1207-1215

  • DOI: 10.1107/S1399004715005106

  • PubMed Abstract: 
  • Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase associated with neuronal development and brain physiology. The DYRK kinases are very unusual with respect to the sequence of the catalytic loop, in which the o ...

    Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase associated with neuronal development and brain physiology. The DYRK kinases are very unusual with respect to the sequence of the catalytic loop, in which the otherwise highly conserved arginine of the HRD motif is replaced by a cysteine. This replacement, along with the proximity of a potential disulfide-bridge partner from the activation segment, implies a potential for redox control of DYRK family activities. Here, the crystal structure of DYRK1A bound to PKC412 is reported, showing the formation of the disulfide bridge and associated conformational changes of the activation loop. The DYRK kinases represent emerging drug targets for several neurological diseases as well as cancer. The observation of distinct activation states may impact strategies for drug targeting. In addition, the characterization of PKC412 binding offers new insights for DYRK inhibitor discovery.


    Organizational Affiliation

    Department of Chemistry, The Norwegian Structural Biology Centre, The Arctic University of Norway, 9037 Tromsø, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity tyrosine-phosphorylation-regulated kinase 1A
A, B, D
368Homo sapiensMutation(s): 0 
Gene Names: DYRK1A (DYRK, MNB, MNBH)
EC: 2.7.12.1
Find proteins for Q13627 (Homo sapiens)
Go to Gene View: DYRK1A
Go to UniProtKB:  Q13627
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dual specificity tyrosine-phosphorylation-regulated kinase 1A
C
368Homo sapiensMutation(s): 0 
Gene Names: DYRK1A (DYRK, MNB, MNBH)
EC: 2.7.12.1
Find proteins for Q13627 (Homo sapiens)
Go to Gene View: DYRK1A
Go to UniProtKB:  Q13627
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2K2
Query on 2K2

Download SDF File 
Download CCD File 
A, B, C, D
PKC412
N-[(5S,6R,7R,9R)-6-methoxy-5-methyl-14-oxo-6,7,8,9,15,16-hexahydro-5H,14H-5,9-epoxy-4b,9a,15-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-7-yl]-N-methylbenzamide
C35 H30 N4 O4
BMGQWWVMWDBQGC-IIFHNQTCSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C
L-PEPTIDE LINKINGC3 H8 N O6 PSER
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2K2Kd: 100 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.597 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.764α = 90.00
b = 87.895β = 90.00
c = 229.921γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
MOLREPphasing
MxCuBEdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-05-20
    Type: Database references
  • Version 1.2: 2015-07-22
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description