1ZOM

Crystal Structure of the Catalytic Domain of Coagulation Factor XI in complex with a peptidomimetic Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design, synthesis, and biological evaluation of peptidomimetic inhibitors of factor XIa as novel anticoagulants.

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

(2006) J Med Chem 49: 7781-7791

  • DOI: 10.1021/jm060978s
  • Primary Citation of Related Structures:  
    1ZOM

  • PubMed Abstract: 
  • Human coagulation factor XIa (FXIa), a serine protease activated by site-specific cleavage of factor XI by thrombin, FXIIa, or autoactivation, is a critical enzyme in the amplification phase of the coagulation cascade. To investigate the potential of ...

    Human coagulation factor XIa (FXIa), a serine protease activated by site-specific cleavage of factor XI by thrombin, FXIIa, or autoactivation, is a critical enzyme in the amplification phase of the coagulation cascade. To investigate the potential of FXIa inhibitors as safe anticoagulants, a series of potent, selective peptidomimetic inhibitors of FXIa were designed and synthesized. Some of these inhibitors showed low nanomolar FXIa inhibitory activity with >1000-fold FXa selectivity and >100-fold thrombin selectivity. The X-ray structure of one of these inhibitors, 36, demonstrates its unique binding interactions with FXIa. Compound 32 caused a doubling of the activated partial thromboplastin time in human plasma at 2.4 microM and was efficacious in a rat model of venous thrombosis. These data suggest that factor XIa plays a significant role in venous thrombosis and may be a suitable target for the development of antithrombotic therapy.


    Organizational Affiliation

    Daiichi Asubio Medical Research Laboratories LLC (DAIAMED), One Kendall Square Building 700, Cambridge, MA 02139, USA. jlin@epixpharma.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
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
NIH Common Fund Data Resources
PHAROS  P03951
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
339
Query on 339

Download Ideal Coordinates CCD File 
A
(S)-2-(3-((R)-1-(4-BROMOPHENYL)ETHYL)UREIDO)-N-((S)-1-((S)-5-GUANIDINO-1-OXO-1-(THIAZOL-2-YL)PENTAN-2-YLAMINO)-3-METHYL-1-OXOBUTAN-2-YL)-5-UREIDOPENTANAMIDE
C29 H45 Br N10 O5 S
HWZOXFNZLMNLSU-MNAPGUCWSA-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 %)
339IC50 :  30   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.932α = 90
b = 120.932β = 90
c = 120.932γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance