3TBG

Human cytochrome P450 2D6 with two thioridazines bound in active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Contributions of Ionic Interactions and Protein Dynamics to Cytochrome P450 2D6 (CYP2D6) Substrate and Inhibitor Binding.

Wang, A.Stout, C.D.Zhang, Q.Johnson, E.F.

(2015) J Biol Chem 290: 5092-5104

  • DOI: 10.1074/jbc.M114.627661
  • Primary Citation of Related Structures:  
    3TBG, 3TDA, 4WNT, 4WNU, 4WNV, 4WNW

  • PubMed Abstract: 
  • P450 2D6 contributes significantly to the metabolism of >15% of the 200 most marketed drugs. Open and closed crystal structures of P450 2D6 thioridazine complexes were obtained using different crystallization conditions. The protonated piperidine moiety of thioridazine forms a charge-stabilized hydrogen bond with Asp-301 in the active sites of both complexes ...

    P450 2D6 contributes significantly to the metabolism of >15% of the 200 most marketed drugs. Open and closed crystal structures of P450 2D6 thioridazine complexes were obtained using different crystallization conditions. The protonated piperidine moiety of thioridazine forms a charge-stabilized hydrogen bond with Asp-301 in the active sites of both complexes. The more open conformation exhibits a second molecule of thioridazine bound in an expanded substrate access channel antechamber with its piperidine moiety forming a charge-stabilized hydrogen bond with Glu-222. Incubation of the crystalline open thioridazine complex with alternative ligands, prinomastat, quinidine, quinine, or ajmalicine, displaced both thioridazines. Quinine and ajmalicine formed charge-stabilized hydrogen bonds with Glu-216, whereas the protonated nitrogen of quinidine is equidistant from Asp-301 and Glu-216 with protonated nitrogen H-bonded to a water molecule in the access channel. Prinomastat is not ionized. Adaptations of active site side-chain rotamers and polypeptide conformations were evident between the complexes, with the binding of ajmalicine eliciting a closure of the open structure reflecting in part the inward movement of Glu-216 to form a hydrogen bond with ajmalicine as well as sparse lattice restraints that would hinder adaptations. These results indicate that P450 2D6 exhibits sufficient elasticity within the crystal lattice to allow the passage of compounds between the active site and bulk solvent and to adopt a more closed form that adapts for binding alternative ligands with different degrees of closure. These crystals provide a means to characterize substrate and inhibitor binding to the enzyme after replacement of thioridazine with alternative compounds.


    Organizational Affiliation

    From the Department of Molecular and Experimental Medicine and johnson@scripps.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2D6A, B, C, D479Homo sapiensMutation(s): 0 
Gene Names: CYP2D6CYP2DL1
EC: 1.14.14.1 (PDB Primary Data), 1.14.14 (UniProt)
Find proteins for P10635 (Homo sapiens)
Explore P10635 
Go to UniProtKB:  P10635
NIH Common Fund Data Resources
PHAROS:  P10635
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
EA [auth D], O [auth A], T [auth B], Z [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
RTZ
Query on RTZ

Download Ideal Coordinates CCD File 
AA [auth D], BA [auth D], E [auth A], F [auth A], P [auth B], Q [auth B], U [auth C], V [auth C]10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine
C21 H26 N2 S2
KLBQZWRITKRQQV-MRXNPFEDSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
N [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], S [auth B], Y [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth D], G [auth A], H [auth A], I [auth A], R [auth B], W [auth C], X [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.19α = 90
b = 191.96β = 90
c = 249.48γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2015-03-11
    Changes: Database references