6H1T

Structure of the BM3 heme domain in complex with clotrimazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs.

Jeffreys, L.N.Poddar, H.Golovanova, M.Levy, C.W.Girvan, H.M.McLean, K.J.Voice, M.W.Leys, D.Munro, A.W.

(2019) Sci Rep 9: 1577-1577

  • DOI: 10.1038/s41598-018-37330-y
  • Primary Citation of Related Structures:  
    6H1O, 6H1T, 6H1S, 6H1L

  • PubMed Abstract: 
  • Flavocytochrome P450 BM3 is a natural fusion protein constructed of cytochrome P450 and NADPH-cytochrome P450 reductase domains. P450 BM3 binds and oxidizes several mid- to long-chain fatty acids, typically hydroxylating these lipids at the ω-1, ω-2 and ω-3 positions ...

    Flavocytochrome P450 BM3 is a natural fusion protein constructed of cytochrome P450 and NADPH-cytochrome P450 reductase domains. P450 BM3 binds and oxidizes several mid- to long-chain fatty acids, typically hydroxylating these lipids at the ω-1, ω-2 and ω-3 positions. However, protein engineering has led to variants of this enzyme that are able to bind and oxidize diverse compounds, including steroids, terpenes and various human drugs. The wild-type P450 BM3 enzyme binds inefficiently to many azole antifungal drugs. However, we show that the BM3 A82F/F87V double mutant (DM) variant binds substantially tighter to numerous azole drugs than does the wild-type BM3, and that their binding occurs with more extensive heme spectral shifts indicative of complete binding of several azoles to the BM3 DM heme iron. We report here the first crystal structures of P450 BM3 bound to azole antifungal drugs - with the BM3 DM heme domain bound to the imidazole drugs clotrimazole and tioconazole, and to the triazole drugs fluconazole and voriconazole. This is the first report of any protein structure bound to the azole drug tioconazole, as well as the first example of voriconazole heme iron ligation through a pyrimidine nitrogen from its 5-fluoropyrimidine ring.


    Organizational Affiliation

    Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom. andrew.munro@manchester.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional cytochrome P450/NADPH--P450 reductaseA, B, C, D458Priestia megateriumMutation(s): 2 
Gene Names: BTA37_15100
EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for A0A1Q8UP87 (Bacillus megaterium)
Explore A0A1Q8UP87 
Go to UniProtKB:  A0A1Q8UP87
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A], HA [auth D], O [auth B], Z [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CL6 (Subject of Investigation/LOI)
Query on CL6

Download Ideal Coordinates CCD File 
AA [auth C], F [auth A], IA [auth D], P [auth B]1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE
C22 H17 Cl N2
VNFPBHJOKIVQEB-UHFFFAOYSA-N
 Ligand Interaction
MPO (Subject of Investigation/LOI)
Query on MPO

Download Ideal Coordinates CCD File 
LA [auth D], R [auth B]3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
GA [auth C], X [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth C] , CA [auth C] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , JA [auth D] , KA [auth D] , 
BA [auth C],  CA [auth C],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  JA [auth D],  KA [auth D],  Q [auth B],  Y [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
PA [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
DA [auth C] , EA [auth C] , FA [auth C] , K [auth A] , L [auth A] , M [auth A] , MA [auth D] , N [auth A] , 
DA [auth C],  EA [auth C],  FA [auth C],  K [auth A],  L [auth A],  M [auth A],  MA [auth D],  N [auth A],  NA [auth D],  OA [auth D],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CL6 Binding MOAD:  6H1T Kd: 3.28e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.408α = 90
b = 70.747β = 95.31
c = 209.644γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K001884/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release