6VKG

Human carbonic anhydrase IX mimic with Epacadostat bound

• PDB DOI: https://doi.org/10.2210/pdb6VKG/pdb

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


• Deposited: 2020-01-20 Released: 2020-03-04 
• Deposition Author(s): Peat, T.S., Carta, F., Supuran, C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.167 
• R-Value Work: 0.127 

Starting Model: experimental

Literature

X-ray crystallography of Epacadostat in adduct with Carbonic Anhydrase IX.

Angeli, A., Peat, T.S., Selleri, S., Saleh Alfawaz Altamimi, A., Supuran, C.T., Carta, F.

(2020) Bioorg Chem 97: 103669-103669

• PubMed: 32088421 
• DOI: https://doi.org/10.1016/j.bioorg.2020.103669
• Primary Citation of Related Structures:  
  6VKG


• PubMed Abstract: 
  

  Epacadostat (EPA), a new and promising anti-cancer small molecule is firmly established as selective inhibitor of the enzyme indoleamine 2,3-dioxygenase 1 (IDO1). The X-Ray structure of the human CA IX mimic in complex with EPA is investigated here for the first time and compared to previously reported EPA-CA II adduct. The structural information obtained are all in agreement with the in vitro kinetic data which accounted for a selective inhibition of the CA IX over the CA II isoform.

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Organizational Affiliation: 

University of Florence, NEUROFARBA Dept., Pharmaceutical and Nutraceutical Section, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy; Centre of Advanced Research in Bionanoconjugates and Biopolymers Department, "Petru Poni" Institute of Macromolecular Chemistry, Iasi, Romania.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 29.92 kDa 
• Atom Count: 2,377 
• Modelled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
human carbonic anhydrase IX mimic	A	260	Homo sapiens	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BBJ (Subject of Investigation/LOI)	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
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.167 
• R-Value Work: 0.127 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.979	α = 90
b = 41.436	β = 104.117
c = 72.122	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Currently 6VKG does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Peat, T.S., Carta, F., Supuran, C.T.

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description