6UNM

CYP3A4 bound to an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report

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This is version 1.4 of the entry. See complete history


Literature

An increase in side-group hydrophobicity largely improves the potency of ritonavir-like inhibitors of CYP3A4.

Samuels, E.R.Sevrioukova, I.F.

(2020) Bioorg Med Chem 28: 115349-115349

  • DOI: https://doi.org/10.1016/j.bmc.2020.115349
  • Primary Citation of Related Structures:  
    6UNE, 6UNG, 6UNH, 6UNI, 6UNJ, 6UNK, 6UNL, 6UNM

  • PubMed Abstract: 

    Identification of structural determinants required for potent inhibition of drug-metabolizing cytochrome P450 3A4 (CYP3A4) could help develop safer drugs and more effective pharmacoenhancers. We utilize a rational inhibitor design to decipher structure-activity relationships in analogues of ritonavir, a highly potent CYP3A4 inhibitor marketed as pharmacoenhancer. Analysis of compounds with the R 1 side-group as phenyl or naphthalene and R 2 as indole or naphthalene in different stereo configuration showed that (i) analogues with the R 2 -naphthalene tend to bind tighter and inhibit CYP3A4 more potently than the R 2 -phenyl/indole containing counterparts; (ii) stereochemistry becomes a more important contributing factor, as the bulky side-groups limit the ability to optimize protein-ligand interactions; (iii) the relationship between the R 1 /R 2 configuration and preferential binding to CYP3A4 is complex and depends on the side-group functionality/interplay and backbone spacing; and (iv) three inhibitors, 5a-b and 7d, were superior to ritonavir (IC 50 of 0.055-0.085 μM vs. 0.130 μM, respectively).


  • Organizational Affiliation

    Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3900, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 3A4
A, B
487Homo sapiensMutation(s): 0 
Gene Names: CYP3A4CYP3A3
EC: 1.14.14.1 (PDB Primary Data), 1.14.14.56 (PDB Primary Data), 1.14.14.73 (PDB Primary Data), 1.14.14.55 (PDB Primary Data)
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
QDP (Subject of Investigation/LOI)
Query on QDP

Download Ideal Coordinates CCD File 
D [auth A]tert-butyl [(2S)-1-(naphthalen-1-yl)-3-{[(2S)-3-(naphthalen-1-yl)-1-oxo-1-{(E)-[2-(pyridin-3-yl)ethylidene]amino}propan-2-yl]sulfanyl}propan-2-yl]carbamate
C38 H39 N3 O3 S
WPQAJKXCNNRUNA-QBJSWQKPSA-N
HEM
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.53α = 90
b = 97.91β = 123.57
c = 92.3γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES025767

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Derived calculations
  • Version 1.2: 2020-02-26
    Changes: Database references
  • Version 1.3: 2020-03-04
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description