3BG8

Crystal structure of Factor XIa in complex with Clavatadine A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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
  • Primary Citation of Related Structures:  
    3BG8

  • 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIa light chainA238Homo sapiensMutation(s): 0 
Gene Names: F11
EC: 3.4.21.27
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
NIH Common Fund Data Resources
PHAROS  P03951
GTEx  ENSG00000088926
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
INH
Query on INH
Download Ideal Coordinates 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 Ideal Coordinates CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
INHIC50 :  1300   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.716α = 90
b = 120.716β = 90
c = 120.716γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

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
    Changes: Version format compliance