7O9W | pdb_00007o9w

Encequidar-bound human P-glycoprotein in complex with UIC2-Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7O9W

This is version 1.4 of the entry. See complete history

Literature

Discovery and Characterization of Potent Dual P-Glycoprotein and CYP3A4 Inhibitors: Design, Synthesis, Cryo-EM Analysis, and Biological Evaluations.

Urgaonkar, S.Nosol, K.Said, A.M.Nasief, N.N.Bu, Y.Locher, K.P.Lau, J.Y.N.Smolinski, M.P.

(2022) J Med Chem 65: 191-216

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01272
  • Primary Citation Related Structures: 
    7O9W

  • PubMed Abstract: 

    Targeted concurrent inhibition of intestinal drug efflux transporter P-glycoprotein (P-gp) and drug metabolizing enzyme cytochrome P450 3A4 (CYP3A4) is a promising approach to improve oral bioavailability of their common substrates such as docetaxel, while avoiding side effects arising from their pan inhibitions. Herein, we report the discovery and characterization of potent small molecule inhibitors of P-gp and CYP3A4 with encequidar (minimally absorbed P-gp inhibitor) as a starting point for optimization. To aid in the design of these dual inhibitors, we solved the high-resolution cryo-EM structure of encequidar bound to human P-gp. The structure guided us to prudently decorate the encequidar scaffold with CYP3A4 pharmacophores, leading to the identification of several analogues with dual potency against P-gp and CYP3A4. In vivo , dual P-gp and CYP3A4 inhibitor 3a improved the oral absorption of docetaxel by 3-fold as compared to vehicle, while 3a itself remained poorly absorbed.


  • Organizational Affiliation
    • Athenex Inc., Conventus Building, Buffalo, New York 14203, United States.

Macromolecule Content 

  • Total Structure Weight: 191.71 kDa 
  • Atom Count: 12,618 
  • Modeled Residue Count: 1,614 
  • Deposited Residue Count: 1,725 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multidrug resistance protein 11,280Homo sapiensMutation(s): 1 
Gene Names: ABCB1MDR1PGY1
EC: 7.6.2.2 (PDB Primary Data), 7.6.2.1 (PDB Primary Data)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08183 (Homo sapiens)
Explore P08183 
Go to UniProtKB:  P08183
PHAROS:  P08183
GTEx:  ENSG00000085563 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08183
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
UIC2 Fab-fragment light chain220Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
UIC2 Fab-fragment heavy chain225Mus musculusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V5Q
(Subject of Investigation/LOI)

Query on V5Q



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
~{N}-[2-[2-[4-[2-(6,7-dimethoxy-3,4-dihydro-1~{H}-isoquinolin-2-yl)ethyl]phenyl]-1,2,3,4-tetrazol-5-yl]-4,5-dimethoxy-phenyl]-4-oxidanylidene-2,3-dihydrochromene-2-carboxamide
C38 H38 N6 O7
ZHCQMPGFIGLQSJ-PSXMRANNSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_189111

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2022-01-26
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.4: 2025-07-02
    Changes: Data collection