6QXU | pdb_00006qxu

Human TNKS1 in complex with 6,8-Difluoro-2-[4-(1-hydroxy-1-methyl-ethyl)-phenyl]-3H-quinazolin-4-one

• PDB DOI: https://doi.org/10.2210/pdb6QXU/pdb

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


• Deposited: 2019-03-08 Released: 2019-08-14 
• Deposition Author(s): Musil, D., Lehmann, D., Buchstaller, H.-P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.213 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: other

Literature

Discovery and Optimization of 2-Arylquinazolin-4-ones into a Potent and Selective Tankyrase Inhibitor Modulating Wnt Pathway Activity.

Buchstaller, H.P., Anlauf, U., Dorsch, D., Kuhn, D., Lehmann, M., Leuthner, B., Musil, D., Radtki, D., Ritzert, C., Rohdich, F., Schneider, R., Esdar, C.

(2019) J Med Chem 62: 7897-7909

• PubMed: 31381853 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00656
• Primary Citation Related Structures: 
  6QXU


• PubMed Abstract: 
  

  Tankyrases 1 and 2 (TNKS1/2) are promising pharmacological targets that recently gained interest for anticancer therapy in Wnt pathway dependent tumors. 2-Aryl-quinazolinones were identified and optimized into potent tankyrase inhibitors through SAR exploration around the quinazolinone core and the 4'-position of the phenyl residue. These efforts were supported by analysis of TNKS X-ray and WaterMap structures and resulted in compound 5k , a potent, selective tankyrase inhibitor with favorable pharmacokinetic properties. The X-ray structure of 5k in complex with TNKS1 was solved and confirmed the design hypothesis. Modulation of Wnt pathway activity was demonstrated with this compound in a colorectal xenograft model in vivo .

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Organizational Affiliation: 
• Merck Healthcare KGaA , Global Research & Development , Frankfurter Strasse 250 , 64293 Darmstadt , 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: 24.67 kDa 
• Atom Count: 2,155 
• Modeled Residue Count: 209 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase tankyrase-1	A	211	Homo sapiens	Mutation(s): 0  Gene Names: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95271 (Homo sapiens) Explore O95271  Go to UniProtKB:  O95271
PHAROS:  O95271 GTEx:  ENSG00000173273

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JKN	C [auth A]	6,8-bis(fluoranyl)-2-[4-(2-oxidanylpropan-2-yl)phenyl]-3~{H}-quinazolin-4-one C17 H14 F2 N2 O2 FHBYLOWAINBPRJ-UHFFFAOYSA-N
BME	B [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JKN	BindingDB:  6QXU	IC50: min: 7, max: 10 (nM) from 4 assay(s)
		EC50: min: 319, max: 320 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.213 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.94	α = 90
b = 94.64	β = 90
c = 62.34	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Musil, D., Lehmann, D., Buchstaller, H.-P.

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description