3RF4

Ancylostoma ceylanicum mif in complex with furosemide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Drug Repositioning and Pharmacophore Identification in the Discovery of Hookworm MIF Inhibitors.

Cho, Y.Vermeire, J.J.Merkel, J.S.Leng, L.Du, X.Bucala, R.Cappello, M.Lolis, E.

(2011) Chem Biol 18: 1089-1101

  • DOI: https://doi.org/10.1016/j.chembiol.2011.07.011
  • Primary Citation of Related Structures:  
    3RF4, 3RF5

  • PubMed Abstract: 

    The screening of bioactive compound libraries can be an effective approach for repositioning FDA-approved drugs or discovering new pharmacophores. Hookworms are blood-feeding, intestinal nematode parasites that infect up to 600 million people worldwide. Vaccination with recombinant Ancylostoma ceylanicum macrophage migration inhibitory factor (rAceMIF) provided partial protection from disease, thus establishing a "proof-of-concept" for targeting AceMIF to prevent or treat infection. A high-throughput screen (HTS) against rAceMIF identified six AceMIF-specific inhibitors. A nonsteroidal anti-inflammatory drug (NSAID), sodium meclofenamate, could be tested in an animal model to assess the therapeutic efficacy in treating hookworm disease. Furosemide, an FDA-approved diuretic, exhibited submicromolar inhibition of rAceMIF tautomerase activity. Structure-activity relationships of a pharmacophore based on furosemide included one analog that binds similarly to the active site, yet does not inhibit the Na-K-Cl symporter (NKCC1) responsible for diuretic activity.


  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor
A, B, C
116Ancylostoma ceylanicumMutation(s): 0 
Gene Names: ACEMIF
UniProt
Find proteins for A4GRE3 (Ancylostoma ceylanicum)
Explore A4GRE3 
Go to UniProtKB:  A4GRE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4GRE3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FUN
Query on FUN

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
R [auth C]
5-(AMINOSULFONYL)-4-CHLORO-2-[(2-FURYLMETHYL)AMINO]BENZOIC ACID
C12 H11 Cl N2 O5 S
ZZUFCTLCJUWOSV-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
L [auth B],
S [auth C],
T [auth C]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
M [auth B]
N [auth B]
U [auth C]
F [auth A],
G [auth A],
M [auth B],
N [auth B],
U [auth C],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
O [auth B]
P [auth B]
Q [auth B]
H [auth A],
I [auth A],
O [auth B],
P [auth B],
Q [auth B],
W [auth C],
X [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
FUN PDBBind:  3RF4 Ki: 560 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.69α = 90
b = 86.69β = 90
c = 115.481γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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: 2011-10-12
    Type: Initial release
  • Version 1.1: 2012-12-05
    Changes: Derived calculations
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description