3KW4

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

Structural Biology Knowledgebase: 3KW4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 3KW4

Classification: OXIDOREDUCTASE

Total Structure Weight: 57522.83

Macromolecule Entities
Molecule Chains Length Organism Details
Cytochrome P450 2B4 A 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
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CH0
Query on CH0

A 2-{[(3alpha,5alpha,7alpha,8alpha,10alpha,12alpha,17alpha)- 3,12-bis{2-[(4-O-alpha-D-glucopyranosyl-beta- D-glucopyranosyl)oxy]ethoxy}cholan-7-yl]oxy}ethyl 4- O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
3,7,12-tris[(-D-maltopyranosyl)ethyloxy]cholane (Synonym)
C66 H114 O36
YGUVIEOMNBFSRV-GLUVFYGUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CM5
Query on CM5

A 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL- BETA-D-GLUCOPYRANOSIDE; CYMAL-5 (Synonym)
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TIC
Query on TIC

A ticlopidine
5, (Synonym)
C14 H14 Cl N S
PHWBOXQYWZNQIN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.195
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.50 α = 90.00
b = 93.50 β = 90.00
c = 137.07 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-11-30
  • Released Date: 2010-09-15
  • Deposition author(s): Gay, S.C., Maekawa, K., Roberts, A.G., Hong, W.-X., Zhang, Q., Stout, C.D., Halpert, J.R.

Revision History

  • 2011-08-31
    Type: Atom nomenclature | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4