6G35

Crystal structure of haspin in complex with 5-bromotubercidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Halogen-Aromatic pi Interactions Modulate Inhibitor Residence Times.

Heroven, C.Georgi, V.Ganotra, G.K.Brennan, P.Wolfreys, F.Wade, R.C.Fernandez-Montalvan, A.E.Chaikuad, A.Knapp, S.

(2018) Angew. Chem. Int. Ed. Engl. 57: 7220-7224

  • DOI: 10.1002/anie.201801666
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Prolonged drug residence times may result in longer lasting drug efficacy, improved pharmacodynamic properties and "kinetic selectivity" over off-targets with fast drug dissociation rates. However, few strategies have been elaborated to rationally mo ...

    Prolonged drug residence times may result in longer lasting drug efficacy, improved pharmacodynamic properties and "kinetic selectivity" over off-targets with fast drug dissociation rates. However, few strategies have been elaborated to rationally modulate drug residence time and thereby to integrate this key property into the drug development process. Here, we show that the interaction between a halogen moiety on an inhibitor and an aromatic residue in the target protein can significantly increase inhibitor residence time. By using the interaction of the serine/threonine kinase haspin with 5-iodotubercidin (5-iTU) derivatives as a model for an archetypal active state (type I) kinase-inhibitor binding mode, we demonstrate that inhibitor residence times markedly increase with the size and polarizability of the halogen atom. This key interaction is dependent on the interactions with an aromatic residue in the gatekeeper position and we observe this interaction in other kinases with an aromatic gatekeeper residue. We provide a detailed mechanistic characterization of the halogen-aromatic π interactions in the haspin-inhibitor complexes by means of kinetic, thermodynamic, and structural measurements along with binding energy calculations. Since halogens are frequently used in drugs and aromatic residues are often present in the binding sites of proteins, our results provide a compelling rationale for introducing aromatic-halogen interactions to prolong drug-target residence times.


    Organizational Affiliation

    University of Oxford, UNITED KINGDOM.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase haspin
A
357Homo sapiensMutation(s): 0 
Gene Names: HASPIN (GSG2)
EC: 2.7.11.1
Find proteins for Q8TF76 (Homo sapiens)
Go to Gene View: HASPIN
Go to UniProtKB:  Q8TF76
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

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A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
EKK
Query on EKK

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Download CCD File 
A
5-bromotubercidin
C11 H13 Br N4 O4
ZWTPRQXZXQEKFT-IOSLPCCCSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
CO
Query on CO

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Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.301α = 90.00
b = 78.760β = 90.00
c = 79.300γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references
  • Version 1.2: 2018-06-13
    Type: Data collection, Database references