5EXN

FACTOR XIA (C500S [C122S]) IN COMPLEX WITH THE INHIBITOR methyl ~{N}-[4-[2-[(1~{S})-1-[[(~{E})-3-[5-chloranyl-2-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]amino]-2-phenyl-ethyl]pyridin-4-yl]phenyl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 

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:  
  • Also Cited By: 6C0S, 5QCN, 5QCM, 5QCL, 5QCK, 5Q0H, 5Q0G, 5Q0F, 5Q0E, 5Q0D, 5WB6

  • 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 ...

    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
    • 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
    • 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) A.C.S.Med.Chem.Lett. 6: 590
    • 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
    • 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
    • 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. Electronic address: james.corte@bms.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XIa light chain
A
238Homo sapiensMutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5SU
Query on 5SU

Download SDF File 
Download CCD File 
A
methyl ~{N}-[4-[2-[(1~{S})-1-[[(~{E})-3-[5-chloranyl-2-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]amino]-2-phenyl-ethyl]pyridin-4-yl]phenyl]carbamate
C31 H26 Cl N7 O3
ZBUQQUJRHVSUJI-CWBDRXANSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.890α = 90.00
b = 69.120β = 90.00
c = 85.320γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTER-TNTrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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