9BBB

Human CYP3A4 bound to an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9BBB/pdb

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


• Deposited: 2024-04-05 Released: 2024-07-03 
• 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: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Starting Model: experimental

Literature

Interaction of CYP3A4 with the inhibitor cobicistat: Structural and mechanistic insights and comparison with ritonavir

Sevrioukova, I.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.15 kDa 
• Atom Count: 3,646 
• Modelled Residue Count: 439 
• 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) Go to UniProtKB:  P08684
PHAROS:  P08684 GTEx:  ENSG00000160868

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1APA (Subject of Investigation/LOI)	C [auth A]	cobicistat C40 H53 N7 O5 S2 ZCIGNRJZKPOIKD-CQXVEOKZSA-N
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.82	α = 90
b = 101.95	β = 90
c = 126.22	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
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: 2024-07-03
  Type: Initial release