5QQO

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(5E,8S)-8-[(6R)-6-(3-chlorophenyl)-2-oxo-1,3-oxazinan-3-yl]-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure based design of macrocyclic factor XIa inhibitors: Discovery of cyclic P1 linker moieties with improved oral bioavailability.

Clark, C.G.Rossi, K.A.Corte, J.R.Fang, T.Smallheer, J.M.De Lucca, I.Nirschl, D.S.Orwat, M.J.Pinto, D.J.P.Hu, Z.Wang, Y.Yang, W.Jeon, Y.Ewing, W.R.Myers Jr., J.E.Sheriff, S.Lou, Z.Bozarth, J.M.Wu, Y.Rendina, A.Harper, T.Zheng, J.Xin, B.Xiang, Q.Luettgen, J.M.Seiffert, D.A.Wexler, R.R.Lam, P.Y.S.

(2019) Bioorg.Med.Chem.Lett. 29: 126604-126604

  • DOI: 10.1016/j.bmcl.2019.08.008
  • Primary Citation of Related Structures:  
  • Also Cited By: 5QTU, 5QTT

  • PubMed Abstract: 
  • This manuscript describes the discovery of a series of macrocyclic inhibitors of FXIa with oral bioavailability. Assisted by structure based drug design and ligand bound X-ray crystal structures, the group linking the P1 moiety to the macrocyclic cor ...

    This manuscript describes the discovery of a series of macrocyclic inhibitors of FXIa with oral bioavailability. Assisted by structure based drug design and ligand bound X-ray crystal structures, the group linking the P1 moiety to the macrocyclic core was modified with the goal of reducing H-bond donors to improve pharmacokinetic performance versus 9. This effort resulted in the discovery of several cyclic P1 linkers, exemplified by 10, that are constrained mimics of the bioactive conformation displayed by the acrylamide linker of 9. These cyclic P1 linkers demonstrated enhanced bioavailability and improved potency.


    Related Citations: 
    • Macrocyclic inhibitors of Factor XIa: Discovery of alkyl-substituted macrocyclic amide linkers with improved potency.
      Corte, J.R.,Yang, W.,Fang, T.,Wang, Y.,Osuna, H.,Lai, A.,Ewing, W.R.,Rossi, K.A.,Myers Jr., J.E.,Sheriff, S.,Lou, Z.,Zheng, J.J.,Harper, T.W.,Bozarth, J.M.,Wu, Y.,Luettgen, J.M.,Seiffert, D.A.,Quan, M.L.,Wexler, R.R.,Lam, P.Y.S.
      (2017) Bioorg. Med. Chem. Lett. 27: 3833
    • 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
    • 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.,Orwat, M.J.,Rendina, A.R.,Luettgen, J.M.,Rossi, K.A.,Wei, A.,Ramamurthy, V.,Myers Jr., J.E.,Sheriff, S.,Narayanan, R.,Harper, T.W.,Zheng, J.J.,Li, Y.X.,Seiffert, D.A.,Wexler, R.R.,Quan, M.L.
      (2016) Bioorg. Med. Chem. 24: 2257
    • 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
    • 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
    • Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties.
      Pinto, D.J.,Smallheer, J.M.,Corte, J.R.,Austin, E.J.,Wang, C.,Fang, T.,Smith 2nd., 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
    • Structure-Based Design of Macrocyclic Factor XIa Inhibitors: Discovery of the Macrocyclic Amide Linker.
      Corte, J.R.,Fang, T.,Osuna, H.,Pinto, D.J.,Rossi, K.A.,Myers Jr., J.E.,Sheriff, S.,Lou, Z.,Zheng, J.J.,Harper, T.W.,Bozarth, J.M.,Wu, Y.,Luettgen, J.M.,Seiffert, D.A.,Decicco, C.P.,Wexler, R.R.,Quan, M.L.
      (2017) J. Med. Chem. 60: 1060
    • Macrocyclic factor XIa inhibitors.
      Wang, C.,Corte, J.R.,Rossi, K.A.,Bozarth, J.M.,Wu, Y.,Sheriff, S.,Myers Jr., J.E.,Luettgen, J.M.,Seiffert, D.A.,Wexler, R.R.,Quan, M.L.
      (2017) Bioorg. Med. Chem. Lett. 27: 4056
    • Pyridazine and pyridazinone derivatives as potent and selective factor XIa inhibitors.
      Hu, Z.,Wang, C.,Han, W.,Rossi, K.A.,Bozarth, J.M.,Wu, Y.,Sheriff, S.,Myers Jr., J.E.,Luettgen, J.M.,Seiffert, D.A.,Wexler, R.R.,Quan, M.L.
      (2018) Bioorg. Med. Chem. Lett. 28: 987
    • Novel phenylalanine derived diamides as Factor XIa inhibitors.
      Smith 2nd., 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.W.,Bozarth, J.M.,Crain, E.J.,Wei, A.,Ramamurthy, V.,Morin, P.E.,Xin, B.,Zheng, J.,Seiffert, D.A.,Quan, M.L.,Lam, P.Y.S.,Wexler, R.R.,Pinto, D.J.P.
      (2016) Bioorg. Med. Chem. Lett. 26: 472
    • Discovery of a Parenteral Small Molecule Coagulation Factor XIa Inhibitor Clinical Candidate (BMS-962212).
      Pinto, D.J.P.,Orwat, M.J.,Smith 2nd., L.M.,Quan, M.L.,Lam, P.Y.S.,Rossi, K.A.,Apedo, A.,Bozarth, J.M.,Wu, Y.,Zheng, J.J.,Xin, B.,Toussaint, N.,Stetsko, P.,Gudmundsson, O.,Maxwell, B.,Crain, E.J.,Wong, P.C.,Lou, Z.,Harper, T.W.,Chacko, S.A.,Myers Jr., J.E.,Sheriff, S.,Zhang, H.,Hou, X.,Mathur, A.,Seiffert, D.A.,Wexler, R.R.,Luettgen, J.M.,Ewing, W.R.
      (2017) J. Med. Chem. 60: 9703


    Organizational Affiliation

    Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States.,Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States. Electronic address: charles.clark@bms.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XI
A
244Homo sapiensMutation(s): 0 
Gene Names: F11
EC: 3.4.21.27
Find proteins for P03951 (Homo sapiens)
Go to Gene View: F11
Go to UniProtKB:  P03951
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MET-ASP-ASP-ASP-ASP-LYS-MET-ASP-ASN-GLU-CYS-THR-THR-LYS-ILE-LYS-PRO-ARG
H
18Homo sapiensMutation(s): 0 
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
NRJ
Query on NRJ

Download SDF File 
Download CCD File 
A
methyl [(5E,8S)-8-[(6R)-6-(3-chlorophenyl)-2-oxo-1,3-oxazinan-3-yl]-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate
C28 H28 Cl N5 O5
ZRELHZVMHRERCT-KXHVVKIWSA-N
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.860α = 90.00
b = 78.860β = 90.00
c = 106.010γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-05-20 
  • Released Date: 2019-09-18 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references