5F8P | pdb_00005f8p

A Novel Inhibitor of the Obesity-Related Protein FTO

• PDB DOI: https://doi.org/10.2210/pdb5F8P/pdb

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


• Deposited: 2015-12-09 Released: 2016-12-14 
• Deposition Author(s): Chai, J., Zhou, B., Liu, W., Han, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.234 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of FTO-CHTB

Chai, J., Zhou, B., Liu, W., Han, Z.

To be published.

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: 55.49 kDa 
• Atom Count: 3,631 
• Modeled Residue Count: 432 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent dioxygenase FTO	A	476	Homo sapiens	Mutation(s): 0  Gene Names: FTO, KIAA1752 EC: 1.14.11 (PDB Primary Data), 1.14.11.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0B1 (Homo sapiens) Explore Q9C0B1  Go to UniProtKB:  Q9C0B1
PHAROS:  Q9C0B1 GTEx:  ENSG00000140718

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FIJ	C [auth A]	4-chloranyl-6-[(2~{S})-6-chloranyl-2,4,4-trimethyl-7-oxidanyl-3~{H}-chromen-2-yl]benzene-1,3-diol C18 H18 Cl2 O4 VSHLILKLIDPGCI-SFHVURJKSA-N
AKG	D [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	E [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FIJ	BindingDB:  5F8P	IC50: 3.92e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.234 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.218	α = 90
b = 142.218	β = 90
c = 83.028	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Chai, J., Zhou, B., Liu, W., Han, Z.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary