3C3U

Crystal structure of AKR1C1 in complex with NADP and 3,5-dichlorosalicylic acid

• PDB DOI: https://doi.org/10.2210/pdb3C3U/pdb

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


• Deposited: 2008-01-28 Released: 2008-08-26 
• Deposition Author(s): Dhagat, U., El-Kabbani, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Selectivity determinants of inhibitor binding to human 20alpha-hydroxysteroid dehydrogenase: crystal structure of the enzyme in ternary complex with coenzyme and the potent inhibitor 3,5-dichlorosalicylic acid

Dhagat, U., Endo, S., Sumii, R., Hara, A., El-Kabbani, O.

(2008) J Med Chem 51: 4844-4848

• PubMed: 18620380 
• DOI: https://doi.org/10.1021/jm8003575
• Primary Citation of Related Structures:  
  3C3U


• PubMed Abstract: 
  

  The crystal structure of human 20alpha-hydroxysteroid dehydrogenase (AKR1C1) in ternary complex with the coenzyme NADP (+) and the potent inhibitor 3,5-dichlorosalicylic acid was determined at a resolution of 1.8 A. The inhibitor is held in place by a network of hydrogen bonding interactions with the active site residues Tyr55, His117, and His222. The important role of the nonconserved residues Leu54, His222, Leu306, and Leu308 in inhibitor binding and selectivity was determined by site-directed mutagenesis.

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Organizational Affiliation: 

Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia.

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: 37.86 kDa 
• Atom Count: 2,981 
• Modelled Residue Count: 320 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member C1	A	323	Homo sapiens	Mutation(s): 0  Gene Names: AKR1C1, DDH, DDH1 EC: 1.1.1.149 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.209 (UniProt), 1.3.1.20 (UniProt), 1.1.1.51 (UniProt), 1.1.1.62 (UniProt), 1.1.1.357 (UniProt), 1.1.1 (UniProt), 1.1.1.210 (UniProt), 1.1.1.112 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q04828 (Homo sapiens) Explore Q04828  Go to UniProtKB:  Q04828
PHAROS:  Q04828 GTEx:  ENSG00000187134

Small Molecules

Ligands 3 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
C2U	D [auth A]	3,5-dichloro-2-hydroxybenzoic acid C7 H4 Cl2 O3 CNJGWCQEGROXEE-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C2U	BindingDB:  3C3U	Ki: min: 5.9, max: 2800 (nM) from 8 assay(s)
		IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.364	α = 90
b = 84.236	β = 91.26
c = 49.183	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Dhagat, U., El-Kabbani, O.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description