3BG8

Crystal structure of Factor XIa in complex with Clavatadine A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Clavatadine A, a natural product with selective recognition and irreversible inhibition of factor XIa.

Buchanan, M.S.Carroll, A.R.Wessling, D.Jobling, M.Avery, V.M.Davis, R.A.Feng, Y.Xue, Y.Oster, L.Fex, T.Deinum, J.Hooper, J.N.Quinn, R.J.

(2008) J.Med.Chem. 51: 3583-3587

  • DOI: 10.1021/jm800314b

  • PubMed Abstract: 
  • Bioassay-guided fractionation of a CH2Cl2/MeOH extract of the sponge Suberea clavata using the serine protease factor XIa to detect antithrombotic activity led to the isolation of the new marine natural products, clavatadines A and B. Clavatadines A ...

    Bioassay-guided fractionation of a CH2Cl2/MeOH extract of the sponge Suberea clavata using the serine protease factor XIa to detect antithrombotic activity led to the isolation of the new marine natural products, clavatadines A and B. Clavatadines A and B inhibited factor XIa with IC50's of 1.3 and 27 microM, respectively. A crystal structure of protein-inhibitor (clavatadine A) complex was obtained and revealed interesting selective binding and irreversible inhibition of factor XIa. The cocrystal structure provides guidance for the design and synthesis of future factor XIa inhibitors as antithrombotic agents.


    Organizational Affiliation

    Eskitis Institute, Griffith University, Brisbane, Queensland 4111, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XIa light chain
A
238Homo sapiensGene Names: F11
EC: 3.4.21.27
Find proteins for P03951 (Homo sapiens)
Go to Gene View: F11
Go to UniProtKB:  P03951
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
INH
Query on INH

Download SDF File 
Download CCD File 
A
N-(R-CARBOXY-ETHYL)-ALPHA-(S)-(2-PHENYLETHYL)GLYCYL-L-ARGININE-N-PHENYLAMIDE
C25 H35 N6 O4
HDGWGGCPTVXRNA-QMMLZNLJSA-O
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BDNIC50: 120000 nM (99) BINDINGDB
INHIC50: 1300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 120.716α = 90.00
b = 120.716β = 90.00
c = 120.716γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-11-26 
  • Released Date: 2008-12-09 
  • Deposition Author(s): Xue, Y., Oster, L.

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance