4TY7

Factor XIa in complex with the inhibitor (2S)-6-amino-N-{(1S)-1-[4-(3-amino-2H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-2-ethylhexanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Phenylimidazoles as Potent and Selective Inhibitors of Coagulation Factor XIa with in Vivo Antithrombotic Activity.

Hangeland, J.J.Friends, T.J.Rossi, K.A.Smallheer, J.M.Wang, C.Sun, Z.Corte, J.R.Fang, T.Wong, P.C.Rendina, A.R.Barbera, F.A.Bozarth, J.M.Luettgen, J.M.Watson, C.A.Zhang, G.Wei, A.Ramamurthy, V.Morin, P.E.Bisacchi, G.S.Subramaniam, S.Arunachalam, P.Mathur, A.Seiffert, D.A.Wexler, R.R.Quan, M.L.

(2014) J.Med.Chem. 57: 9915-9932

  • DOI: 10.1021/jm5010607
  • Primary Citation of Related Structures:  
  • Also Cited By: 4WXI, 6C0S, 5QCN, 5QCM, 5QCL, 5QCK, 5Q0H, 5Q0G, 5Q0F, 5Q0E, 5Q0D, 5WB6, 5EXL, 4X6P, 4X6O, 4X6N, 4X6M

  • PubMed Abstract: 
  • Novel inhibitors of FXIa containing an (S)-2-phenyl-1-(4-phenyl-1H-imidazol-2-yl)ethanamine core have been optimized to provide compound 16b, a potent, reversible inhibitor of FXIa (Ki = 0.3 nM) having in vivo antithrombotic efficacy in the rabbit AV ...

    Novel inhibitors of FXIa containing an (S)-2-phenyl-1-(4-phenyl-1H-imidazol-2-yl)ethanamine core have been optimized to provide compound 16b, a potent, reversible inhibitor of FXIa (Ki = 0.3 nM) having in vivo antithrombotic efficacy in the rabbit AV-shunt thrombosis model (ID50 = 0.6 mg/kg + 1 mg kg(-1) h(-1)). Initial analog selection was informed by molecular modeling using compounds 11a and 11h overlaid onto the X-ray crystal structure of tetrahydroquinoline 3 complexed to FXIa. Further optimization was achieved by specific modifications derived from careful analysis of the X-ray crystal structure of the FXIa/11h complex. Compound 16b was well tolerated and enabled extensive pharmacologic evaluation of the FXIa mechanism up to the ID90 for thrombus inhibition.


    Related Citations: 
    • Tetrahydroquinoline derivatives as potent and selective factor XIa inhibitors.
      Quan, M.L.,Wong, P.C.,Wang, C.,Woerner, F.,Smallheer, J.M.,Barbera, F.A.,Bozarth, J.M.,Brown, R.L.,Harpel, M.R.,Luettgen, J.M.,Morin, P.E.,Peterson, T.,Ramamurthy, V.,Rendina, A.R.,Rossi, K.A.,Watson, C.A.,Wei, A.,Zhang, G.,Seiffert, D.,Wexler, R.R.
      (2014) J.Med.Chem. 57: 955


    Organizational Affiliation

    Research and Development, Bristol-Myers Squibb , P.O. Box 5400, Princeton, New Jersey 08543, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XI
A
244Homo sapiensMutation(s): 2 
Gene Names: F11
EC: 3.4.21.27
Find proteins for P03951 (Homo sapiens)
Go to Gene View: F11
Go to UniProtKB:  P03951
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
39F
Query on 39F

Download SDF File 
Download CCD File 
A
trans-N-{(1S)-1-[4-(3-amino-2H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-4-(aminomethyl)cyclohexane-1-carboxamide
C26 H30 Cl N7 O
IOLSRAXZCKDSPO-FIKGOQFSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
39FKi: 0.3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.100α = 90.00
b = 79.100β = 90.00
c = 106.300γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
AMoREphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-07-08 
  • Released Date: 2014-12-03 
  • Deposition Author(s): Wei, A.

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-17
    Type: Database references
  • Version 1.2: 2015-02-25
    Type: Derived calculations
  • Version 2.0: 2017-11-22
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary