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PDBsum entry 3bg8
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protein ligands links
Hydrolase PDB id
3bg8

 

 

 

 

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Contents
Protein chain
238 a.a. *
Ligands
G0R-BEN-SO4
SO4 ×4
Waters ×252
* Residue conservation analysis
PDB id:
3bg8
Name: Hydrolase
Title: Crystal structure of factor xia in complex with clavatadine a
Structure: Coagulation factor xia light chain. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: f11. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
Resolution:
1.60Å     R-factor:   0.179     R-free:   0.200
Authors: Y.Xue,L.Oster
Key ref: M.S.Buchanan et al. (2008). Clavatadine A, a natural product with selective recognition and irreversible inhibition of factor XIa. J Med Chem, 51, 3583-3587. PubMed id: 18510371
Date:
26-Nov-07     Release date:   09-Dec-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03951  (FA11_HUMAN) -  Coagulation factor XI from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		625 a.a.
238 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.27  - coagulation factor XIa.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Arg-|-Ala and Arg-|-Val bonds in factor IX to form factor IXa.

 

 
J Med Chem 51:3583-3587 (2008)
PubMed id: 18510371  
 
 
Clavatadine A, a natural product with selective recognition and irreversible inhibition of factor XIa.
M.S.Buchanan, A.R.Carroll, D.Wessling, M.Jobling, V.M.Avery, R.A.Davis, Y.Feng, Y.Xue, L.Oster, T.Fex, J.Deinum, J.N.Hooper, R.J.Quinn.
 
  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 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21439031 L.Rosenbaum, G.Hinselmann, A.Jahn, and A.Zell (2011).
Interpreting linear support vector machine models with heat map molecule coloring.
  J Cheminform, 3, 11.  
20111802 J.W.Blunt, B.R.Copp, M.H.Munro, P.T.Northcote, and M.R.Prinsep (2010).
Marine natural products.
  Nat Prod Rep, 27, 165-237.  
20957265 R.G.Berlinck, A.C.Burtoloso, A.E.Trindade-Silva, S.Romminger, R.P.Morais, K.Bandeira, and C.M.Mizuno (2010).
The chemistry and biology of organic guanidine derivatives.
  Nat Prod Rep, 27, 1871-1907.  
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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