6IQ5 | pdb_00006iq5

Crystal Structure of CYP1B1 and Inhibitor Having Azide Group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.396 (Depositor), 0.440 (DCC) 
  • R-Value Work: 
    0.356 (Depositor), 0.420 (DCC) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design and synthesis of selective CYP1B1 inhibitor via dearomatization of alpha-naphthoflavone.

Kubo, M.Yamamoto, K.Itoh, T.

(2019) Bioorg Med Chem 27: 285-304

  • DOI: https://doi.org/10.1016/j.bmc.2018.11.045
  • Primary Citation of Related Structures:  
    6IQ5

  • PubMed Abstract: 

    Selective cytochrome P450 (CYP) 1B1 inhibition has potential as an anticancer strategy that is unrepresented in the current clinical arena. For development of a selective inhibitor, we focused on the complexity caused by sp 3 -hybridized carbons and synthesized a series of benzo[h]chromone derivatives linked to a non-aromatic B-ring using α-naphthoflavone (ANF) as the lead compound. Ring structure comparison suggested compound 37 as a suitable cyclohexyl-core with improved solubility. Structural evolution of 37 produced the azide-containing cis-49a, which had good properties in three important respects: (1) selectivity for CYP1B1 over CYP1A1 and CYP1A2 (120-times and 150-times, respectively), (2) greater inhibitory potency of >2 times that of ANF, and (3) improved solubility. The corresponding aromatic B-ring compound 59a showed low selectivity and poor solubility. To elucidate the binding mode, we performed X-ray crystal structure analysis, which revealed the interaction mode and explained the subtype selectivity of cis-49a.


  • Organizational Affiliation
    • Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 1B1
A, B
463Homo sapiensMutation(s): 2 
Gene Names: CYP1B1
EC: 1.14.14.1 (PDB Primary Data), 4.2.1.152 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16678 (Homo sapiens)
Explore Q16678 
Go to UniProtKB:  Q16678
PHAROS:  Q16678
GTEx:  ENSG00000138061 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16678
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
AQ0 BindingDB:  6IQ5 IC50: 4.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.396 (Depositor), 0.440 (DCC) 
  • R-Value Work:  0.356 (Depositor), 0.420 (DCC) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.19α = 90
b = 135.19β = 90
c = 302.17γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references