5EXM

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl ~{N}-[4-[2-[(1~{S})-1-[[4-(aminomethyl)cyclohexyl]carbonylamino]-2-phenyl-ethyl]pyridin-4-yl]phenyl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Orally bioavailable pyridine and pyrimidine-based Factor XIa inhibitors: Discovery of the methyl N-phenyl carbamate P2 prime group

Corte, J.R.Fang, T.Pinto, D.J.P.Orwat, M.J.Han, W.Rendina, A.R.Luettgen, J.M.Rossi, K.A.Wei, A.Ramamurthy, V.Myers Jr., J.E.Sheriff, S.Narayanan, R.Harper, T.Zheng, J.J.Li, Y.-X.Seiffert, D.A.Wexler, R.R.Quan, M.L.

(2016) Bioorg Med Chem 24: 2257-2272

  • DOI: 10.1016/j.bmc.2016.03.062
  • Primary Citation of Related Structures:  
    5EXM, 5EXL, 5EXN

  • PubMed Abstract: 
  • Pyridine-based Factor XIa (FXIa) inhibitor (S)-2 was optimized by modifying the P2 prime, P1, and scaffold regions. This work resulted in the discovery of the methyl N-phenyl carbamate P2 prime group which maintained FXIa activity, reduced the number of ...

    Pyridine-based Factor XIa (FXIa) inhibitor (S)-2 was optimized by modifying the P2 prime, P1, and scaffold regions. This work resulted in the discovery of the methyl N-phenyl carbamate P2 prime group which maintained FXIa activity, reduced the number of H-bond donors, and improved the physicochemical properties compared to the amino indazole P2 prime moiety. Compound (S)-17 was identified as a potent and selective FXIa inhibitor that was orally bioavailable. Replacement of the basic cyclohexyl methyl amine P1 in (S)-17 with the neutral p-chlorophenyltetrazole P1 resulted in the discovery of (S)-24 which showed a significant improvement in oral bioavailability compared to the previously reported imidazole (S)-23. Additional improvements in FXIa binding affinity, while maintaining oral bioavailability, was achieved by replacing the pyridine scaffold with either a regioisomeric pyridine or pyrimidine ring system.


    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
    • 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
    • Pyridine and Pyridinone-Based Factor XIa Inhibitors
      Corte, J.R., Fang, T., Hangeland, J.J., Friends, T.J., Rendina, A.R., Luettgen, J.M., Bozarth, J.M., Barbera, F.A., Rossi, K.A., Wei, A., Ramamurthy, V., Morin, P.E., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2015) Bioorg Med Chem Lett 25: 925
    • Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties
      Pinto, D.J.P., Smallheer, J.M., Corte, J.R., Austin, E.J.D., Wang, C., Fang, T., Smith II, L.M., Rossi, K.A., Rendina, A.R., Bozarth, J.M., Zhang, G., Wei, A., Ramamurthy, V., Sheriff, S., Myers Jr., J.E., Morin, P.E., Luettgen, J.M., Seiffert, D.A., Quan, M.L., Wexler, R.R.
      (2015) Bioorg Med Chem Lett 25: 1635
    • Discovery of a Potent Parenterally Administered Factor XIa Inhibitor with Hydroxyquinolin-2(1H)-one as the P2' Moiety
      Hu, Z., Wong, P.C., Gilligan, P.J., Han, W., Pabbisetty, K.B., Bozarth, J.M., Crain, E.J., Harper, T., Luettgen, J.M., Myers Jr., J.E., Ramamurthy, V., Rossi, K.A., Sheriff, S., Watson, C.A., Wei, A., Zheng, J.J., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2015) ACS Med Chem Lett 6: 590
    • Novel phenylalanine derived diamides as Factor XIa inhibitors
      Smith II, L.M., Orwat, M.J., Hu, Z., Han, W., Wang, C., Rossi, K.A., Gilligan, P.J., Pabbisetty, K.B., Osuna, H., Corte, J.R., Rendina, A.R., Luettgen, J.M., Wong, P.C., Narayanan, R., Harper, T., Bozarth, J.M., Crain, E.J., Wei, A., Ramamurthy, V., Morin, P.E., Seiffert, D.A., Quan, M.L., Lam, P.Y.S., Wexler, R.R., Pinto, D.J.P.
      (2015) Bioorg Med Chem Lett --: --

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIa light chain A244Homo sapiensMutation(s): 2 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5ST
Query on 5ST

Download Ideal Coordinates CCD File 
A
methyl ~{N}-[4-[2-[(1~{S})-1-[[4-(aminomethyl)cyclohexyl]carbonylamino]-2-phenyl-ethyl]pyridin-4-yl]phenyl]carbamate
C29 H34 N4 O3
YAJFVXIHHOXQOV-MYIHVTGJSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5STKi:  6.300000190734863   nM  Binding MOAD
5STKi:  6.300000190734863   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.1α = 90
b = 79.1β = 90
c = 106.6γ = 120
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-11-23 
  • Released Date: 2016-04-13 
  • Deposition Author(s): Wei, A.

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references