1DB4

HUMAN S-PLA2 IN COMPLEX WITH INDOLE 8

Structural Biology Knowledgebase: 1DB4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.226

Literature

Macromolecules
Sequence Display for 1DB4

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 14441.63

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHOLIPASE A2 A 124 Homo sapiens EC#: 3.1.1.4 IUBMB
Gene Name(s): PLA2G2A Gene View PLA2B PLA2L RASF-A
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
8IN
Query on 8IN

A [3-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H- INDOL-5-YLOXY)-PROPYL-]-PHOSPHONIC ACID
C21 H25 N2 O5 P
AQEYCNKFBRLUOT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
8IN IC50: 57 - 67000 nM (100) BindingDB

N/A in BindingMoad
IC50: 57 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.226
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 77.01 α = 90.00
b = 77.01 β = 90.00
c = 91.62 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-11-02
  • Released Date: 1999-11-12
  • Deposition author(s): Chirgadze, N.Y., Schevitz, R.W., Wery, J.-P.

Revision History

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