3BG8

Crystal structure of Factor XIa in complex with Clavatadine A

• PDB DOI: https://doi.org/10.2210/pdb3BG8/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


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

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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 

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

• PubMed: 18510371 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.64 kDa 
• Atom Count: 2,179 
• Modelled Residue Count: 238 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XIa light chain	A	238	Homo sapiens	Mutation(s): 0  Gene Names: F11 EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens) Explore P03951  Go to UniProtKB:  P03951
PHAROS:  P03951 GTEx:  ENSG00000088926

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G0R	B [auth A]	N-(4-carbamimidamidobutyl)ethanamide C7 H16 N4 O JMACEDIUUMWDIC-UHFFFAOYSA-N
BEN	C [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 120.716	α = 90
b = 120.716	β = 90
c = 120.716	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 2.0: 2021-10-13
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-10-09
  Changes: Data collection, Structure summary