6IQ5

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 
  • R-Value Work: 0.356 

wwPDB Validation   3D Report Full Report


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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
  • 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 ...

    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. Electronic address: titoh@ac.shoyaku.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 1B1A, B463Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
AQ0 (Subject of Investigation/LOI)
Query on AQ0

Download Ideal Coordinates CCD File 
D [auth A]2-(cis-4-azidocyclohexyl)-4H-naphtho[1,2-b]pyran-4-one
C19 H17 N3 O2
MCMLNAPQDOZTMY-OKILXGFUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.396 
  • R-Value Work: 0.356 
  • 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