6IQ5

Crystal Structure of CYP1B1 and Inhibitor Having Azide Group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.396 
  • R-Value Work: 0.356 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1016/j.bmc.2018.11.045

  • 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 <sup>3 </sup>-hybridized c ...

    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.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: titoh@ac.shoyaku.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 1B1
A, B
463Homo sapiensMutation(s): 0 
Gene Names: CYP1B1
EC: 1.14.14.-
Find proteins for Q16678 (Homo sapiens)
Go to Gene View: CYP1B1
Go to UniProtKB:  Q16678
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AQ0
Query on AQ0

Download SDF File 
Download CCD File 
A
2-(cis-4-azidocyclohexyl)-4H-naphtho[1,2-b]pyran-4-one
C19 H17 N3 O2
MCMLNAPQDOZTMY-OKILXGFUSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.396 
  • R-Value Work: 0.356 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 135.190α = 90.00
b = 135.190β = 90.00
c = 302.170γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
pointlessdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release