7OPS

Crystal structure of haspin in complex with ZW282 (compound 2a)

• PDB DOI: https://doi.org/10.2210/pdb7OPS/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-01 Released: 2021-07-21 
• Deposition Author(s): Chaikuad, A., Anizon, F., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.229 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Synthesis and biological evaluation of Haspin inhibitors: Kinase inhibitory potency and cellular activity.

Zeinyeh, W., Esvan, Y.J., Josselin, B., Defois, M., Baratte, B., Knapp, S., Chaikuad, A., Anizon, F., Giraud, F., Ruchaud, S., Moreau, P.

(2022) Eur J Med Chem 236: 114369-114369

• PubMed: 35447555 
• DOI: https://doi.org/10.1016/j.ejmech.2022.114369
• Primary Citation of Related Structures:  
  7OPS


• PubMed Abstract: 
  

  Haspin (haploid germ cell-specific nuclear protein kinase) offers a potential target for the development of new anticancer drugs. Thus, the identification of new inhibitors targeting this protein kinase is of high interest. However, Haspin inhibitors developed to date show a poor selectivity profile over other protein kinases of the human kinome. Here, we identified a new pyridoquinazoline based inhibitor (4), with excellent inhibitory activity and selectivity for Haspin (IC ₅₀ of 50 nM). We describe the structure-activity relationship study including the evaluation of this inhibitor on a large panel of 486 kinases as well as on immortalized or cancer cell lines. In addition, we determined the binding mode of analog 2a in complex with Haspin using X-ray crystallography.

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Organizational Affiliation: 

Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000, Clermont-Ferrand, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.08 kDa 
• Atom Count: 2,807 
• Modelled Residue Count: 328 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase haspin	A	357	Homo sapiens	Mutation(s): 0  Gene Names: HASPIN, 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
07C (Subject of Investigation/LOI)	B [auth A]	2-methylsulfanyl-10-nitro-pyrido[3,4-g]quinazoline C12 H8 N4 O2 S FAEYQDREFVLABR-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
07C	BindingDB:  7OPS	IC50: 119 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.229 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.13	α = 90
b = 79.106	β = 90
c = 80.245	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Chaikuad, A., Anizon, F., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description