5HTC | pdb_00005htc

Crystal structure of haspin (GSG2) in complex with bisubstrate inhibitor ARC-3372


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.171 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 66MClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Co-crystal structures of the protein kinase haspin with bisubstrate inhibitors.

Lavogina, D.Kestav, K.Chaikuad, A.Heroven, C.Knapp, S.Uri, A.

(2016) Acta Crystallogr F Struct Biol Commun 72: 339-345

  • DOI: https://doi.org/10.1107/S2053230X16004611
  • Primary Citation of Related Structures:  
    5HTB, 5HTC

  • PubMed Abstract: 

    Haspin is a mitotic protein kinase that is responsible for the phosphorylation of Thr3 of histone H3, thereby creating a recognition motif for docking of the chromosomal passenger complex that is crucial for the progression of cell division. Here, two high-resolution models of haspin with previously reported inhibitors consisting of an ATP analogue and a histone H3(1-7) peptide analogue are presented. The structures of the complexes confirm the bisubstrate character of the inhibitors by revealing the signature binding modes of the moieties targeting the ATP-binding site and the protein substrate-binding site of the kinase. This is the first structural model of a bisubstrate inhibitor targeting haspin. The presented structural data represent a model for the future development of more specific haspin inhibitors.


  • Organizational Affiliation

    Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase haspin357Homo sapiensMutation(s): 0 
Gene Names: GSG2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF76 (Homo sapiens)
Explore Q8TF76 
Go to UniProtKB:  Q8TF76
PHAROS:  Q8TF76
GTEx:  ENSG00000177602 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TF76
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ARC-3372 INHIBITORB [auth C]7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
66M
Query on 66M

Download Ideal Coordinates CCD File 
G [auth C](2R)-2-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}butanedioic acid (non-preferred name)
C20 H27 N7 O9
MMQKVHWBTLHGSP-ZXQBGJJXSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.97α = 90
b = 78.903β = 90
c = 81.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 66MClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2016-05-11
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Refinement description