6F20

Complex between MTH1 and compound 1 (a 7-azaindole-4-ester derivative)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Creation of a Novel Class of Potent and Selective MutT Homologue 1 (MTH1) Inhibitors Using Fragment-Based Screening and Structure-Based Drug Design.

Rahm, F.Viklund, J.Tresaugues, L.Ellermann, M.Giese, A.Ericsson, U.Forsblom, R.Ginman, T.Gunther, J.Hallberg, K.Lindstrom, J.Persson, L.B.Silvander, C.Talagas, A.Diaz-Saez, L.Fedorov, O.Huber, K.V.M.Panagakou, I.Siejka, P.Gorjanacz, M.Bauser, M.Andersson, M.

(2018) J Med Chem 61: 2533-2551

  • DOI: 10.1021/acs.jmedchem.7b01884
  • Primary Citation of Related Structures:  
    6F23, 6F22, 6F1X, 6F20

  • PubMed Abstract: 
  • Recent literature has both suggested and questioned MTH1 as a novel cancer target. BAY-707 was just published as a target validation small molecule probe for assessing the effects of pharmacological inhibition of MTH1 on tumor cell survival, both in vitro and in vivo ...

    Recent literature has both suggested and questioned MTH1 as a novel cancer target. BAY-707 was just published as a target validation small molecule probe for assessing the effects of pharmacological inhibition of MTH1 on tumor cell survival, both in vitro and in vivo. (1) In this report, we describe the medicinal chemistry program creating BAY-707, where fragment-based methods were used to develop a series of highly potent and selective MTH1 inhibitors. Using structure-based drug design and rational medicinal chemistry approaches, the potency was increased over 10,000 times from the fragment starting point while maintaining high ligand efficiency and drug-like properties.


    Organizational Affiliation

    Sprint Bioscience AB, Novum , 14157 Huddinge , Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
7,8-dihydro-8-oxoguanine triphosphataseA, B159Homo sapiensMutation(s): 0 
Gene Names: NUDT1MTH1
EC: 3.6.1.55 (PDB Primary Data), 3.6.1.56 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens)
Explore P36639 
Go to UniProtKB:  P36639
PHAROS:  P36639
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C9E (Subject of Investigation/LOI)
Query on C9E

Download Ideal Coordinates CCD File 
C [auth A], K [auth B]Ethyl 1H-pyrrolo[2,3-b]pyridine-4-carboxylate
C10 H10 N2 O2
CKCBQXQNAUHBDX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], N [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C9E BindingDB:  6F20 Kd: 4.95e+4 (nM) from 1 assay(s)
IC50: 9900 (nM) from 1 assay(s)
Binding MOAD:  6F20 Kd: 4.95e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.15α = 90
b = 68.22β = 90
c = 82.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references