6IMZ | pdb_00006imz

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

PDB DOI: https://doi.org/10.2210/pdb6IMZ/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-10-24 Released: 2019-10-30
Deposition Author(s): Yokoyama, T., Kosaka, Y., Matsumoto, K., Kitakami, R., Nabeshima, Y., Mizuguchi, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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.

Macromolecule Content

Total Structure Weight: 20.26 kDa
Atom Count: 1,471
Modeled Residue Count: 162
Deposited Residue Count: 163
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydro-8-oxoguanine triphosphatase	A	163	Homo sapiens	Mutation(s): 0 Gene Names: NUDT1, MTH1 EC: 3.6.1.55 (PDB Primary Data), 3.6.1.56 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36639 (Homo sapiens) Explore P36639 Go to UniProtKB: P36639
PHAROS: P36639 GTEx: ENSG00000106268
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36639
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VGH Query on VGH Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	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		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
O4B Query on O4B Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A]	E [auth A], H [auth A]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C₁₂ H₂₄ O₆ XEZNGIUYQVAUSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain H [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain G [auth A]