9COV

Crystal structure of CYP3A4 bound to an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9COV/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-17 Released: 2025-01-08 
• Deposition Author(s): Sevrioukova, I.F.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.250 
• R-Value Observed: 0.256 

Starting Model: experimental

Literature

Evaluation of larger side-group functionalities and the side/end-group interplay in ritonavir-like inhibitors of CYP3A4

Samuels, E.R., Sevrioukova, I.F.

(2025) Chem Biol Drug Des 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 56.95 kDa 
• Atom Count: 3,552 
• Modelled Residue Count: 431 
• Deposited Residue Count: 487 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 3A4	A	487	Homo sapiens	Mutation(s): 0  Gene Names: CYP3A4, CYP3A3 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
A1A4S (Subject of Investigation/LOI)	C [auth A]	N-[(2S)-1-(1H-indol-3-yl)-3-{[(2R)-1-oxo-3-phenyl-1-{[3-(pyridin-3-yl)propyl]amino}propan-2-yl]sulfanyl}propan-2-yl]pyridine-3-carboxamide C34 H35 N5 O2 S ABZLMAOSAJFABX-BHDXBOSCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.250 
• R-Value Observed: 0.256 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.399	α = 90
b = 99.77	β = 90
c = 122.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-08 
Deposition Author(s): Sevrioukova, I.F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES025767

Revision History  

• Version 1.0: 2025-01-08
  Type: Initial release