4I5X

Crystal Structure Of AKR1B10 Complexed With NADP+ And Flufenamic acid

• PDB DOI: https://doi.org/10.2210/pdb4I5X/pdb

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


• Deposited: 2012-11-29 Released: 2013-10-23 
• Deposition Author(s): Zhang, L., Zheng, X., Chen, S., Zhai, J., Zhang, H., Zhao, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Inhibitor selectivity between aldo-keto reductase superfamily members AKR1B10 and AKR1B1: Role of Trp112 (Trp111)

Zhang, L., Zhang, H., Zhao, Y., Li, Z., Chen, S., Zhai, J., Chen, Y., Xie, W., Wang, Z., Li, Q., Zheng, X., Hu, X.

(2013) FEBS Lett 587: 3681-3686

• PubMed: 24100137 
• DOI: https://doi.org/10.1016/j.febslet.2013.09.031
• Primary Citation of Related Structures:  
  4GQG, 4I5X, 4JIH, 4JII, 4JIR


• PubMed Abstract: 
  

  The antineoplastic target aldo-keto reductase family member 1B10 (AKR1B10) and the critical polyol pathway enzyme aldose reductase (AKR1B1) share high structural similarity. Crystal structures reported here reveal a surprising Trp112 native conformation stabilized by a specific Gln114-centered hydrogen bond network in the AKR1B10 holoenzyme, and suggest that AKR1B1 inhibitors could retain their binding affinities toward AKR1B10 by inducing Trp112 flip to result in an "AKR1B1-like" active site in AKR1B10, while selective AKR1B10 inhibitors can take advantage of the broader active site of AKR1B10 provided by the native Trp112 side-chain orientation.

---

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)

Macromolecule Content

• Total Structure Weight: 37.31 kDa 
• Atom Count: 2,799 
• Modelled Residue Count: 318 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member B10	A	318	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B10 EC: 1.1.1 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.54 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60218 (Homo sapiens) Explore O60218  Go to UniProtKB:  O60218
PHAROS:  O60218 GTEx:  ENSG00000198074

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
FLF	B [auth A]	2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID C14 H10 F3 N O2 LPEPZBJOKDYZAD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FLF	BindingDB:  4I5X	IC50: min: 760, max: 9.60e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.402	α = 90
b = 89.402	β = 90
c = 77.874	γ = 120

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Zhang, L., Zheng, X., Chen, S., Zhai, J., Zhang, H., Zhao, Y.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description