4MQ2

The crystal structure of DYRK1a with a bound pyrido[2,3-d]pyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Pyrido[2,3-d]pyrimidines: Discovery and preliminary SAR of a novel series of DYRK1B and DYRK1A inhibitors.

Anderson, K.Chen, Y.Chen, Z.Dominique, R.Glenn, K.He, Y.Janson, C.Luk, K.C.Lukacs, C.Polonskaia, A.Qiao, Q.Railkar, A.Rossman, P.Sun, H.Xiang, Q.Vilenchik, M.Wovkulich, P.Zhang, X.

(2013) Bioorg Med Chem Lett 23: 6610-6615

  • DOI: https://doi.org/10.1016/j.bmcl.2013.10.055
  • Primary Citation of Related Structures:  
    4MQ1, 4MQ2

  • PubMed Abstract: 

    DYRK1B is a kinase over-expressed in certain cancer cells (including colon, ovarian, pancreatic, etc.). Recent publications have demonstrated inhibition of DYRK1B could be an attractive target for cancer therapy. From a data-mining effort, the team has discovered analogues of pyrido[2,3-d]pyrimidines as potent enantio-selective inhibitors of DYRK1B. Cells treated with a tool compound from this series showed the same cellular effects as down regulation of DYRK1B with siRNA. Such effects are consistent with the proposed mechanism of action. Progress of the SAR study is presented.


  • Organizational Affiliation

    Discovery Chemistry, Hoffmann-La Roche Inc., pRED, Pharma Research & Early Development, 340 Kingsland Street, Nutley, NJ 07110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity tyrosine-phosphorylation-regulated kinase 1A
A, B, C, D
361Homo sapiensMutation(s): 0 
Gene Names: DYRK1ADYRKMNBMNBH
EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens)
Explore Q13627 
Go to UniProtKB:  Q13627
PHAROS:  Q13627
GTEx:  ENSG00000157540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13627
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2C4
Query on 2C4

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
P [auth C],
R [auth D]
methyl 4-chloro-3-{[(2-methoxy-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl)carbonyl]amino}benzoate
C17 H13 Cl N4 O5
SIVLENRHVVVPKJ-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
K [auth B]
L [auth B]
Q [auth C]
F [auth A],
G [auth A],
K [auth B],
L [auth B],
Q [auth C],
S [auth D]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
2C4 BindingDB:  4MQ2 IC50: 97 (nM) from 1 assay(s)
PDBBind:  4MQ2 IC50: 97 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.097α = 90
b = 65.161β = 115.01
c = 138.426γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection