4YVV

Crystal structure of AKR1C3 complexed with glibenclamide

• PDB DOI: https://doi.org/10.2210/pdb4YVV/pdb

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


• Deposited: 2015-03-20 Released: 2015-11-25 
• Deposition Author(s): Zhao, Y., Zheng, X., Zhang, H., Hu, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

In vitro inhibition of AKR1Cs by sulphonylureas and the structural basis

Zhao, Y., Zheng, X., Zhang, H., Zhai, J., Zhang, L., Li, C., Zeng, K., Chen, Y., Li, Q., Hu, X.

(2015) Chem Biol Interact 240: 310-315

• PubMed: 26362498 
• DOI: https://doi.org/10.1016/j.cbi.2015.09.006
• Primary Citation of Related Structures:  
  4YVP, 4YVV, 4YVX, 4ZFC


• PubMed Abstract: 
  

  Recent epidemiological studies show conflicting data for the first-line anti-diabetic sulphonylureas drugs in treating cancer progression in type II diabetes patients. How sulphonylureas promote or diminish tumor growth is not fully understood. Here, we report that seven sulphonylureas exhibit different in vitro inhibition towards AKR1Cs (AKR1C1, AKR1C2, AKR1C3), which are critical steroid hormone metabolism enzymes that are related to prostate cancer, breast cancer and endometrial diseases. Interactions of the sulphonylureas and AKR1Cs were analyzed by X-ray crystallography.

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Organizational Affiliation: 

School of Pharmaceutical Sciences & Centre for Cellular and Structural Biology of Sun Yat-sen University, Guangzhou 510006, China.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.29 kDa 
• Atom Count: 5,536 
• Modelled Residue Count: 630 
• Deposited Residue Count: 646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member C3	A, B	323	Homo sapiens	Mutation(s): 0  Gene Names: AKR1C3 EC: 1 (PDB Primary Data), 1.1.1.357 (PDB Primary Data), 1.1.1.112 (PDB Primary Data), 1.1.1.188 (PDB Primary Data), 1.1.1.239 (PDB Primary Data), 1.1.1.64 (PDB Primary Data), 1.3.1.20 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.62 (UniProt), 1.1.1 (UniProt), 1.1.1.210 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42330 (Homo sapiens) Explore P42330  Go to UniProtKB:  P42330
PHAROS:  P42330 GTEx:  ENSG00000196139

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GBM	D [auth A], F [auth B]	5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide C23 H28 Cl N3 O5 S ZNNLBTZKUZBEKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.103	α = 74.49
b = 48.973	β = 86.64
c = 83.367	γ = 69.44

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Zhao, Y., Zheng, X., Zhang, H., Hu, X.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2016-04-06
  Changes: Non-polymer description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary