6G3A | pdb_00006g3a

Crystal structure of haspin F605T mutant in complex with 5-iodotubercidin

• PDB DOI: https://doi.org/10.2210/pdb6G3A/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-03-24 Released: 2018-04-18 
• Deposition Author(s): Heroven, C., Chaikuad, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Knapp, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.175 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

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

• PubMed: 29601130 
• DOI: https://doi.org/10.1002/anie.201801666
• Primary Citation Related Structures: 
  6G33, 6G34, 6G35, 6G36, 6G37, 6G38, 6G39, 6G3A


• PubMed Abstract: 
  

  Prolonged drug residence times may result in longer-lasting drug efficacy, improved pharmacodynamic properties, and "kinetic selectivity" over off-targets with high 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. Herein, 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. The halogen-aromatic π interactions in the haspin-inhibitor complexes were characterized by means of kinetic, thermodynamic, and structural measurements along with binding-energy calculations.

---

Organizational Affiliation: 
• Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK.
Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, 13353, Berlin, Germany.
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118, Heidelberg, Germany.
Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University, 69120, Heidelberg, Germany.
Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg University, 69120, Heidelberg, Germany.
Interdisciplinary Center for Scientific Computing, Heidelberg University, 69120, Heidelberg, Germany.
Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, 60438, Frankfurt am Main, Germany.
Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, 60438, Frankfurt am Main, Germany.
German Cancer Network (DKTK), Frankfurt/Mainz site, 60438, Frankfurt am Main, Germany.

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: 41.48 kDa 
• Atom Count: 2,916 
• Modeled 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): 1  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5ID	D [auth A]	(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL C11 H13 I N4 O4 WHSIXKUPQCKWBY-IOSLPCCCSA-N
IOD	B [auth A], C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.175 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.351	α = 90
b = 78.7	β = 90
c = 79.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Heroven, C., Chaikuad, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2018-05-16
  Changes: Data collection, Database references
• Version 1.2: 2018-06-13
  Changes: Data collection, Database references
• Version 2.0: 2018-07-04
  Changes: Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description