2FDA

Crystal Structure of the Catalytic Domain of Human Coagulation Factor XIa in Complex with alpha-Ketothiazole Arginine Derived Ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthesis, SAR exploration, and X-ray crystal structures of factor XIa inhibitors containing an alpha-ketothiazole arginine

Deng, H.Bannister, T.D.Jin, L.Babine, R.E.Quinn, J.Nagafuji, P.Celatka, C.A.Lin, J.Lazarova, T.I.Rynkiewicz, M.J.Bibbins, F.Pandey, P.Gorga, J.Meyers, H.V.Abdel-Meguid, S.S.Strickler, J.E.

(2006) Bioorg Med Chem Lett 16: 3049-3054

  • DOI: 10.1016/j.bmcl.2006.02.052
  • Primary Citation of Related Structures:  
    1ZPC, 1ZPB, 2FDA

  • PubMed Abstract: 
  • Using an alpha-ketothiazole arginine moiety as a key recognition element, a series of small peptidomimetic molecules was designed and synthesized, and their co-crystal structures with factor XIa were studied in an effort to develop smaller, less peptidic inhibitors as antithrombotic agents ...

    Using an alpha-ketothiazole arginine moiety as a key recognition element, a series of small peptidomimetic molecules was designed and synthesized, and their co-crystal structures with factor XIa were studied in an effort to develop smaller, less peptidic inhibitors as antithrombotic agents.


    Related Citations: 
    • Mutation of Surface Residues to Promote Crystallization of Activated Factor Xi as a Complex with Benzamidine: An Essential Step for the Iterative Structure-Based Design of Factor Xi Inhibitors
      Jin, L., Pandey, P., Babine, R.E., Weaver, D.T., Abdel-Meguid, S.S., Strickler, J.E.
      (2005) Acta Crystallogr D Biol Crystallogr 61: 1418

    Organizational Affiliation

    Department of Medicinal Chemistry, Daiichi Asubio Medical Research Laboratories, LLC (DAIAMED), One Kendall Square, Bldg 700, Cambridge, MA 02139, USA. hongfeng.deng@praecis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIA238Homo sapiensMutation(s): 4 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
682
Query on 682

Download Ideal Coordinates CCD File 
E [auth A]N~2~-(AMINOCARBONYL)-N~1~-{4-{[AMINO(IMINO)METHYL]AMINO}-1-[HYDROXY(1,3-THIAZOL-2-YL)METHYL]BUTYL}VALINAMIDE
C15 H27 N7 O3 S
WOLWXHDYZAKRKB-DCAQKATOSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BCT
Query on BCT

Download Ideal Coordinates CCD File 
B [auth A], D [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
682IC50 :  501.9999694824219   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.318α = 90
b = 121.318β = 90
c = 121.318γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance