7ZH8

DYRK1a in Complex with a Bromo-Triazolo-Pyridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Screening of a Halogen-Enriched Fragment Library Leads to Unconventional Binding Modes.

Dammann, M.Stahlecker, J.Zimmermann, M.O.Klett, T.Rotzinger, K.Kramer, M.Coles, M.Stehle, T.Boeckler, F.M.

(2022) J Med Chem 65: 14539-14552

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00951
  • Primary Citation of Related Structures:  
    7ZH8

  • PubMed Abstract: 

    We conceived the Halogen-Enriched Fragment Library (HEFLib) to investigate the potential of halogen bonds in the early stages of drug discovery. As the number of competitive interactions increases with ligand size, we reasoned that a binding mode relying on halogen bonding is more likely for fragments than highly decorated molecules. Thus, fragments could feature unexplored binding modes. We screened the HEFLib against the human kinase DYRK1a and verified micromolar binding fragments via isothermal titration calorimetry (ITC). The crystal structure of one fragment revealed a noncanonical binding mode, despite the fragment's classical hinge binding motif. In addition, the fragment occupies a secondary binding site. Both binding modes feature a halogen bond, which we evaluated by ab initio calculations. Structure-affinity relationship (SAR) from a set of analogues improves the affinity, provides a promising fragment-growth vector, and highlights the benefits and applicability of halogen bonds in early lead development.


  • Organizational Affiliation

    Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany.


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
382Homo sapiensMutation(s): 0 
Gene Names: DYRK1ADYRKMNBMNBH
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13627
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
AB [auth D],
EA [auth B],
L [auth A],
SA [auth C]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
DA [auth B],
M [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
IWU (Subject of Investigation/LOI)
Query on IWU

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E [auth A]
G [auth A]
KA [auth C]
MA [auth C]
V [auth B]
E [auth A],
G [auth A],
KA [auth C],
MA [auth C],
V [auth B],
W [auth B],
WA [auth D],
XA [auth D]
6-bromanyl-3H-[1,2,3]triazolo[4,5-b]pyridine
C5 H3 Br N4
YKWWQNVTTSHHGH-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
F [auth A],
LA [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
RA [auth C],
ZA [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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H [auth A]
JA [auth C]
NA [auth C]
OA [auth C]
Y [auth B]
H [auth A],
JA [auth C],
NA [auth C],
OA [auth C],
Y [auth B],
YA [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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BB [auth D]
CB [auth D]
DB [auth D]
FA [auth B]
GA [auth B]
BB [auth D],
CB [auth D],
DB [auth D],
FA [auth B],
GA [auth B],
HA [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
TA [auth C],
UA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
K [auth A]
PA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
K [auth A],
PA [auth C],
QA [auth C],
X [auth B],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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IA [auth B],
S [auth A],
T [auth A],
U [auth A],
VA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 245.004α = 90
b = 64.663β = 115.577
c = 147.308γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary