2AZ5

Crystal Structure of TNF-alpha with a small molecule inhibitor

  • Classification: CYTOKINE
  • Deposited: 2005-09-09 Released: 2005-11-29
  • Deposition author(s): He, M.M.
  • Organism: Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)

Structural Biology Knowledgebase: 2AZ5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2AZ5

Classification: CYTOKINE

Total Structure Weight: 66738.44

Macromolecule Entities
Molecule Chains Length Organism Details
Tumor necrosis factor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin) [Contains: Tumor necrosis factor, membrane form; Tumor necrosis factor, soluble form] A, B, C, D 148 Homo sapiens Gene Name(s): TNF Gene View TNFA TNFSF2

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
307
Query on 307

A, C 6,7-DIMETHYL-3-[(METHYL{2-[METHYL({1-[3-(TRIFLUOROMETHYL)PHENYL]- 1H-INDOL-3-YL}METHYL)AMINO]ETHYL}AMINO)METHYL]- 4H-CHROMEN-4-ONE
C32 H32 F3 N3 O2
JZNXLPPJRFFECJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
307 Kd: 3 - 13000 nM (100) BindingDB

IC50: 22000 nM  BindingMOAD
Kd: 5360 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.220
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 165.25 α = 90.00
b = 165.25 β = 90.00
c = 63.73 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-09-09
  • Released Date: 2005-11-29
  • Deposition author(s): He, M.M.

Revision History

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