6IC2 | pdb_00006ic2

Polypharmacology of Epacadostat: a Potent and Selective Inhibitor of the Tumor Associated Carbonic Anhydrases IX and XII

• PDB DOI: https://doi.org/10.2210/pdb6IC2/pdb

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


• Deposited: 2018-12-01 Released: 2019-05-15 
• Deposition Author(s): Angeli, A., Ferraroni, M., Supuran, C.T., Carta, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.268 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

Polypharmacology of epacadostat: a potent and selective inhibitor of the tumor associated carbonic anhydrases IX and XII.

Angeli, A., Ferraroni, M., Nocentini, A., Selleri, S., Gratteri, P., Supuran, C.T., Carta, F.

(2019) Chem Commun (Camb) 55: 5720-5723

• PubMed: 31038135 
• DOI: https://doi.org/10.1039/c8cc09568j
• Primary Citation Related Structures: 
  6IC2


• PubMed Abstract: 
  

  Epacadostat (EPA), a selective indoleamine-2,3-dioxygenase 1 (IDO1) inhibitor, has been investigated in vitro as a human (h) Carbonic Anhydrase Inhibitor (CAI). The kinetic data clearly show, for the first time, EPA to be a highly effective and selective inhibitor for the tumor-associated isoforms hCA IX/XII. We report the high resolution X-ray crystal structure of the EPA-hCA II adduct, and assessed its binding mode to CA IX/XII by means of computational techniques. EPA may exert antitumor effects also due to the potent inhibition of the tumor-associated CAs.

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Organizational Affiliation: 
• University of Florence, NEUROFARBA Dept., Sezione di Farmaceutica e Nutraceutica, Via Ugo Schiff 6, Sesto Fiorentino, 50019, Florence, Italy. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 29.79 kDa 
• Atom Count: 2,335 
• Modeled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BBJ	C [auth A]	N-(3-bromo-4-fluorophenyl)-N'-hydroxy-4-{[2-(sulfamoylamino)ethyl]amino}-1,2,5-oxadiazole-3-carboximidamide C11 H13 Br F N7 O4 S FBKMWOJEPMPVTQ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.268 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.418	α = 90
b = 41.385	β = 104.54
c = 72.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Angeli, A., Ferraroni, M., Supuran, C.T., Carta, F.

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection, Database references
• Version 1.2: 2024-05-15
  Changes: Advisory, Data collection, Database references