6BD8 | pdb_00006bd8

Crystal structure of human CYP3A4 bound to an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6BD8/pdb

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


• Deposited: 2017-10-21 Released: 2017-12-13 
• Deposition Author(s): Sevrioukova, I.
• 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: 2.38 Å
• R-Value Free: 
  0.269 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Interaction of the rationally designed ritonavir-like inhibitors with human cytochrome P450 3A4: Impact of the side group interplay

Samuels, E.R., Sevrioukova, I.F.

(2017) Mol Pharm 

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: 56.89 kDa 
• Atom Count: 3,834 
• Modeled Residue Count: 457 
• 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: 1.14.13 (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

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
D81	C [auth A]	S-{(2S)-2-[(1-tert-butoxyethenyl)amino]-3-phenylpropyl}-N~2~-cyclopentyl-N-[(pyridin-3-yl)methyl]-L-cysteinamide C29 H42 N4 O2 S XSOXMZJIQQXOTI-SVBPBHIXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.269 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.74	α = 90
b = 101.29	β = 90
c = 123.61	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: 2017-12-13 
Deposition Author(s): Sevrioukova, I.

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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: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Author supporting evidence
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description