3W1W | pdb_00003w1w

Protein-drug complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.229 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3W1W

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Salicylic Acid induces mitochondrial injury by inhibiting ferrochelatase heme biosynthesis activity

Gupta, V.Liu, S.Ando, H.Ishii, R.Tateno, S.Kaneko, Y.Yugami, M.Sakamoto, S.Yamaguchi, Y.Nureki, O.Handa, H.

(2013) Mol Pharmacol 84: 824-833

  • DOI: https://doi.org/10.1124/mol.113.087940
  • Primary Citation Related Structures: 
    3W1W

  • PubMed Abstract: 

    Salicylic acid is a classic nonsteroidal anti-inflammatory drug. Although salicylic acid also induces mitochondrial injury, the mechanism of its antimitochondrial activity is not well understood. In this study, by using a one-step affinity purification scheme with salicylic acid-immobilized beads, ferrochelatase (FECH), a homodimeric enzyme involved in heme biosynthesis in mitochondria, was identified as a new molecular target of salicylic acid. Moreover, the cocrystal structure of the FECH-salicylic acid complex was determined. Structural and biochemical studies showed that salicylic acid binds to the dimer interface of FECH in two possible orientations and inhibits its enzymatic activity. Mutational analysis confirmed that Trp301 and Leu311, hydrophobic amino acid residues located at the dimer interface, are directly involved in salicylic acid binding. On a gel filtration column, salicylic acid caused a shift in the elution profile of FECH, indicating that its conformational change is induced by salicylic acid binding. In cultured human cells, salicylic acid treatment or FECH knockdown inhibited heme synthesis, whereas salicylic acid did not exert its inhibitory effect in FECH knockdown cells. Concordantly, salicylic acid treatment or FECH knockdown inhibited heme synthesis in zebrafish embryos. Strikingly, the salicylic acid-induced effect in zebrafish was partially rescued by FECH overexpression. Taken together, these findings illustrate that FECH is responsible for salicylic acid-induced inhibition of heme synthesis, which may contribute to its antimitochondrial and anti-inflammatory function. This study establishes a novel aspect of the complex pharmacological effects of salicylic acid.


  • Organizational Affiliation
    • Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan (V.G., S.L., H.A., S.T., Y.K., M.Y., S.S., Y.Y., H.H.); and Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan (R.I., O.N.).

Macromolecule Content 

  • Total Structure Weight: 89.18 kDa 
  • Atom Count: 6,474 
  • Modeled Residue Count: 718 
  • Deposited Residue Count: 742 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferrochelatase, mitochondrial
A, B
371Homo sapiensMutation(s): 1 
Gene Names: FECH
EC: 4.99.1.1 (PDB Primary Data), 4.98.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P22830 (Homo sapiens)
Explore P22830 
Go to UniProtKB:  P22830
PHAROS:  P22830
GTEx:  ENSG00000066926 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22830
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHD

Query on CHD



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
I [auth A]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth B]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SAL

Query on SAL



Download:Ideal Coordinates CCD File
G [auth A]2-HYDROXYBENZOIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.229 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.531α = 90
b = 93.627β = 90
c = 110.287γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description