1DB5

HUMAN S-PLA2 IN COMPLEX WITH INDOLE 6

Structural Biology Knowledgebase: 1DB5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1DB5

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 14405.66

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (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
6IN
Query on 6IN

A 4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H- INDOL-5-YLOXY)-BUTYRIC ACID
C22 H24 N2 O4
STENXUCYNKOBHJ-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 %)
6IN IC50: 152 - 69000 nM (100) BindingDB

N/A in BindingMoad
IC50: 152 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.196
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 76.36 α = 90.00
b = 76.36 β = 90.00
c = 91.53 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

  • 2012-02-29
    Type: Citation | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4