6BDH | pdb_00006bdh

Crystal structure of human CYP3A4 bound to an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6BDH/pdb

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


• Deposited: 2017-10-23 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: 2.25 Å
• R-Value Free: 
  0.280 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.210 (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: 3,656 
• Modeled 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: 1.14.13 (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) Membrane Entity: Yes
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
DEV	C [auth A]	tert-butyl [(2S)-1-{[(2S)-3-oxo-2-(phenylamino)-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}-3-phenylpropan-2-yl]carbamate C29 H36 N4 O3 S CVZKJZYGCLDJTJ-IZZNHLLZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.280 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.37	α = 90
b = 99.88	β = 90
c = 125.93	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