3ME6

Crystal structure of cytochrome 2B4 in complex with the anti-platelet drug clopidogrel

Structural Biology Knowledgebase: 3ME6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.178

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ME6

Classification: OXIDOREDUCTASE

Total Structure Weight: 220432.44

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome P450 2B4 A, B, C, D 476 Oryctolagus cuniculus EC#: 1.14.14.1 IUBMB
Mutation: E21A, ΔF3, ΔS4, ΔL5, ΔL6, ΔL7, ΔL8, ΔL9, ΔA10, ΔF11, ΔL12, ΔA13, ΔG14, ΔL15, ΔL16, ΔL17, ΔL18, ΔL19, ΔF20, ΔR21, G22K, H23K, P24T, K25S, A26S, H27K, R29K, P221S, H226Y
Gene Name(s): CYP2B4

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B, C, D PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CGE
Query on CGE

A, B, C, D Clopidogrel
7-dihydrothieno[3, (Synonym)
C16 H16 Cl N O2 S
GKTWGGQPFAXNFI-HNNXBMFYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.178
  • Space Group: P 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 234.49 α = 90.00
b = 234.49 β = 90.00
c = 57.32 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-31
  • Released Date: 2010-09-15
  • Deposition author(s): Gay, S.C., Roberts, A.G., Maekawa, K., Talakad, J.C., Hong, W.X., Zhang, Q., Stout, C.D., Halpert, J.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4