3G5N

Triple ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole

Structural Biology Knowledgebase: 3G5N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.218

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3G5N

Classification: OXIDOREDUCTASE

Total Structure Weight: 223935.06

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, ΔA14, 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 3 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)
CM5
Query on CM5

A, B, C, D 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PB2
Query on PB2

A, B, C, D 1-(biphenyl-4-ylmethyl)-1H-imidazole
C16 H14 N2
DLYMRVCQTVOYEW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PB2 N/A in BindingDB
IC50: 35 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.218
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 86.70 α = 90.00
b = 152.53 β = 90.00
c = 181.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-02-05
  • Released Date: 2009-05-12
  • Deposition author(s): Gay, S.C., Sun, L., Maekawa, K., Halpert, J.R., Stout, C.D.

Revision History

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