5G5J

Crystal structure of human CYP3A4 bound to metformin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.chembiol.2017.08.009
  • Primary Citation of Related Structures:  
    5G5J

  • 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 (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 Medicine Hematology, Oncology and Transplantation Division and Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME P450 3A4487Homo sapiensMutation(s): 0 
EC: 1.14.13 (PDB Primary Data), 1.14.13.157 (PDB Primary Data), 1.14.13.32 (PDB Primary Data), 1.14.14.1 (PDB Primary Data), 1.14.13.67 (PDB Primary Data), 1.14.13.97 (PDB Primary Data), 1.14.14.73 (UniProt), 1.14.14.56 (UniProt), 1.14.14.55 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P08684 (Homo sapiens)
Explore P08684 
Go to UniProtKB:  P08684
PHAROS:  P08684
GTEx:  ENSG00000160868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08684
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
MF8
Query on MF8

Download Ideal Coordinates CCD File 
B [auth A]Metformin
C4 H11 N5
XZWYZXLIPXDOLR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77α = 90
b = 101.07β = 90
c = 128.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description