6A7A

AKR1C1 complexed with new inhibitor with novel scaffold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.162 

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Ligand Structure Quality Assessment 


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Literature

Screening, synthesis, crystal structure, and molecular basis of 6-amino-4-phenyl-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitriles as novel AKR1C3 inhibitors.

Zheng, X.Jiang, Z.Li, X.Zhang, C.Li, Z.Wu, Y.Wang, X.Zhang, C.Luo, H.B.Xu, J.Wu, D.

(2018) Bioorg Med Chem 26: 5934-5943

  • DOI: 10.1016/j.bmc.2018.10.044
  • Primary Citation of Related Structures:  
    6IJX, 6A7A, 6A7B

  • PubMed Abstract: 
  • AKR1C3 is a promising therapeutic target for castration-resistant prostate cancer. Herein, an evaluation of in-house library discovered substituted pyranopyrazole as a novel scaffold for AKR1C3 inhibitors. Preliminary SAR exploration identified its derivative 19d as the most promising compound with an IC 50 of 0 ...

    AKR1C3 is a promising therapeutic target for castration-resistant prostate cancer. Herein, an evaluation of in-house library discovered substituted pyranopyrazole as a novel scaffold for AKR1C3 inhibitors. Preliminary SAR exploration identified its derivative 19d as the most promising compound with an IC 50 of 0.160 μM among the 23 synthesized molecules. Crystal structure studies revealed that the binding mode of the pyranopyrazole scaffold is different from the current inhibitors. Hydroxyl, methoxy and nitro group at the C4-phenyl substituent together anchor the inhibitor to the oxyanion site, while the core of the scaffold dramatically enlarges but partially occupies the SP pockets with abundant hydrogen bond interactions. Strikingly, the inhibitor undergoes a conformational change to fit AKR1C3 and its homologous protein AKR1C1. Our results suggested that conformational changes of the receptor and the inhibitor should both be considered during the rational design of selective AKR1C3 inhibitors. Detailed binding features obtained from molecular dynamics simulations helped to finally elucidate the molecular basis of 6-amino-4-phenyl-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitriles as AKR1C3 inhibitors, which would facilitate the future rational inhibitor design and structural optimization.


    Organizational Affiliation

    School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China. Electronic address: wudeyan3@mail.sysu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member C1A338Homo sapiensMutation(s): 0 
Gene Names: AKR1C1DDHDDH1
EC: 1.1.1 (PDB Primary Data), 1.1.1.149 (PDB Primary Data), 1.1.1.112 (PDB Primary Data), 1.3.1.20 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q04828 (Homo sapiens)
Explore Q04828 
Go to UniProtKB:  Q04828
PHAROS:  Q04828
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
9S0 (Subject of Investigation/LOI)
Query on 9S0

Download Ideal Coordinates CCD File 
C [auth A](4R)-6-amino-4-(4-hydroxy-3-methoxy-5-nitrophenyl)-3-propyl-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile
C17 H17 N5 O5
RWKXJNWNTFOJQN-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.124α = 90
b = 83.517β = 90.32
c = 48.938γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81602968

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references