4WRH

AKR1C3 complexed with breakdown product of N-(tert-butyl)-2-(2-chloro-4-(((3-mercapto-5-methyl-4H-1,2,4-triazol-4-yl)amino)methyl)-6-methoxyphenoxy)acetamide

• PDB DOI: https://doi.org/10.2210/pdb4WRH/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-24 Released: 2014-11-05 
• Deposition Author(s): Squire, C.J., Flanagan, J.U., Yosaatmadja, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.187 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Breakdown product of N-(tert-butyl)-2-(2-chloro-4-(((3-mercapto-5-methyl-4H-1,2,4-triazol-4-yl)amino)methyl)-6-methoxyphenoxy)acetamide trapped in active site of AKR1C3

Yosaatmadja, Y., Ko, R.-W., Flanagan, J.U., Squire, C.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.26 kDa 
• Atom Count: 2,813 
• Modelled Residue Count: 316 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member C3	A	331	Homo sapiens	Mutation(s): 0  Gene Names: AKR1C3, DDH1, HSD17B5, KIAA0119, PGFS 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
YY2	C [auth A]	2-[4-(aminomethyl)-2-chloro-6-methoxyphenoxy]-N-tert-butylacetamide C14 H21 Cl N2 O3 HEOFBSUCMHLHRB-UHFFFAOYSA-N
YY1	D [auth A]	5-methyl-4H-1,2,4-triazole-3-thiol C3 H5 N3 S OUZCWDMJTKYHCA-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.187 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.509	α = 90
b = 63.503	β = 90
c = 95.567	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Squire, C.J., Flanagan, J.U., Yosaatmadja, Y.

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy