Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 37896.81 
• Atom Count: 2637 
• Residue Count: 323 
• Unique protein chains: 1

3NTY

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

• DOI: 10.2210/pdb3NTY/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2010-07-06 Released: 2011-04-13 
• Deposition Author(s): Dhagat, U., El-Kabbani, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.253 
• R-Value Work: 0.185 

Literature

Probing the inhibitor selectivity pocket of human 20 alpha-hydroxysteroid dehydrogenase (AKR1C1) with X-ray crystallography and site-directed mutagenesis

El-Kabbani, O., Dhagat, U., Soda, M., Endo, S., Matsunaga, T., Hara, A.

(2011) Bioorg.Med.Chem.Lett. 21: 2564-2567

• PubMed: 21414777 
• DOI: 10.1016/j.bmcl.2011.01.076


• PubMed Abstract: 
  

Human 20α-hydroxysteroid dehydrogenase (AKR1C1) is an important drug target due to its role in the development of lung and endometrial cancers, premature birth and neuronal disorders. We report the crystal structure of AKR1C1 complexed with the first structure-based designed inhibitor 3-chloro-5-phenylsalicylic acid (K(i)=0.86 nM) bound in the active site. The binding of 3-chloro-5-phenylsalicylic acid to AKR1C1 resulted in a conformational change in the side chain of Phe311 to accommodate the bulky phenyl ring substituent at the 5-position of the inhibitor. The contributions of the nonconserved residues Leu54, Leu306, Leu308 and Phe311 to the binding were further investigated by site-directed mutagenesis, and the effects of the mutations on the K(i) value were determined. The Leu54Val and Leu306Ala mutations resulted in 6- and 81-fold increases, respectively, in K(i) values compared to the wild-type enzyme, while the remaining mutations had little or no effects.

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Organizational Affiliation: 

Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aldo-keto reductase family 1 member C1	A	323	Homo sapiens	Mutation(s): 0  Gene Names: AKR1C1 (DDH, DDH1) EC: 1.1.1.-
Find proteins for Q04828 (Homo sapiens) Go to Gene View: AKR1C1 Go to UniProtKB:  Q04828

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NAP	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
5P3	A	5-chloro-4-hydroxybiphenyl-3-carboxylic acid 5-Phenyl,3-chlorosalicylic acid C13 H9 Cl O3 RJMZIUFNDNYWDU-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5P3	Ki: 0.9 - 21 nM (100) BINDINGDB
5P3	IC50: 100 nM (100) BINDINGDB
5P3	Ki: 0.86 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.253 
• R-Value Work: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 39.607	α = 90.00
b = 84.052	β = 91.41
c = 49.051	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-06 
• Released Date: 2011-04-13 
• Deposition Author(s): Dhagat, U., El-Kabbani, O.

Revision History 

• Version 1.0: 2011-04-13
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance