5G5J

Crystal structure of human CYP3A4 bound to metformin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Heme Binding Biguanides Target Cytochrome P450-Dependent Cancer Cell Mitochondria.

Guo, Z.Sevrioukova, I.F.Denisov, I.G.Zhang, X.Chiu, T.L.Thomas, D.G.Hanse, E.A.Cuellar, R.A.D.Grinkova, Y.V.Langenfeld, V.W.Swedien, D.S.Stamschror, J.D.Alvarez, J.Luna, F.Galvan, A.Bae, Y.K.Wulfkuhle, J.D.Gallagher, R.I.Petricoin, E.F.Norris, B.Flory, C.M.Schumacher, R.J.O'Sullivan, M.G.Cao, Q.Chu, H.Lipscomb, J.D.Atkins, W.M.Gupta, K.Kelekar, A.Blair, I.A.Capdevila, J.H.Falck, J.R.Sligar, S.G.Poulos, T.L.Georg, G.I.Ambrose, E.Potter, D.A.

(2017) Cell Chem Biol 24: 1259-1275.e6

  • DOI: 10.1016/j.chembiol.2017.08.009

  • PubMed Abstract: 
  • The mechanisms by which cancer cell-intrinsic CYP monooxygenases promote tumor progression are largely unknown. CYP3A4 was unexpectedly associated with breast cancer mitochondria and synthesized arachidonic acid (AA)-derived epoxyeicosatrienoic acids ...

    The mechanisms by which cancer cell-intrinsic CYP monooxygenases promote tumor progression are largely unknown. CYP3A4 was unexpectedly associated with breast cancer mitochondria and synthesized arachidonic acid (AA)-derived epoxyeicosatrienoic acids (EETs), which promoted the electron transport chain/respiration and inhibited AMPKα. CYP3A4 knockdown activated AMPKα, promoted autophagy, and prevented mammary tumor formation. The diabetes drug metformin inhibited CYP3A4-mediated EET biosynthesis and depleted cancer cell-intrinsic EETs. Metformin bound to the active-site heme of CYP3A4 in a co-crystal structure, establishing CYP3A4 as a biguanide target. Structure-based design led to discovery of N1-hexyl-N5-benzyl-biguanide (HBB), which bound to the CYP3A4 heme with higher affinity than metformin. HBB potently and specifically inhibited CYP3A4 AA epoxygenase activity. HBB also inhibited growth of established ER + mammary tumors and suppressed intratumoral mTOR. CYP3A4 AA epoxygenase inhibition by biguanides thus demonstrates convergence between eicosanoid activity in mitochondria and biguanide action in cancer, opening a new avenue for cancer drug discovery.


    Organizational Affiliation

    Department of Pharmacology, Center for Cancer Pharmacology and Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.,Department of Medicine Hematology, Oncology and Transplantation Division and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Departments of Biochemistry and Pharmacology, University of Texas Southwestern, Dallas, TX, USA.,Center for Translational Medicine, University of Minnesota, Minneapolis, MN, USA.,Division of Biostatistics and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,College of Veterinary Medicine and Masonic Cancer Center, University of Minnesota, St. Paul, MN, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA.,Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University, Nashville, TN, USA.,Department of Pathology and Cancer Center, University of Michigan, Ann Arbor, MN, USA.,Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA.,Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA, USA.,Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Department of Medicine Hematology, Oncology and Transplantation Division and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerologia-Instituto de Investigaciones Biomedicas, UNAM, Mexico, Mexico.,Department of Pathology, Yeungnam University, Daegu, Korea.,Department of Medicine Hematology, Oncology and Transplantation Division and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA. Electronic address: dapotter@umn.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME P450 3A4
A
487Homo sapiensMutation(s): 0 
Gene Names: CYP3A4 (CYP3A3)
EC: 1.14.14.-
Find proteins for P08684 (Homo sapiens)
Go to Gene View: CYP3A4
Go to UniProtKB:  P08684
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MF8
Query on MF8

Download SDF File 
Download CCD File 
A
Metformin
N,N-Dimethylimidodicarbonimidic diamide
C4 H11 N5
XZWYZXLIPXDOLR-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
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: 2.6 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.202 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.000α = 90.00
b = 101.070β = 90.00
c = 128.370γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-05-25 
  • Released Date: 2017-06-07 
  • Deposition Author(s): Sevrioukova, I.

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references