6IMZ

Crystal structure of MTH1 in complex with 18-Crown-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crown Ethers as Transthyretin Amyloidogenesis Inhibitor

Yokoyama, T.Kosaka, Y.Matsumoto, K.Kitakami, R.Nabeshima, Y.Mizuguchi, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
7,8-dihydro-8-oxoguanine triphosphataseA163Homo 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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VGH (Subject of Investigation/LOI)
Query on VGH

Download Ideal Coordinates CCD File 
F [auth A]3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine
C21 H22 Cl2 F N5 O
KTEIFNKAUNYNJU-GFCCVEGCSA-N
 Ligand Interaction
O4B (Subject of Investigation/LOI)
Query on O4B

Download Ideal Coordinates CCD File 
E [auth A], H [auth A]1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE
C12 H24 O6
XEZNGIUYQVAUSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.434α = 90
b = 66.434β = 90
c = 140.182γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release