5QTU

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(3R,7S)-7-{[1-(3-chloro-2-fluorophenyl)-5-methyl-1H-imidazole-4-carbonyl]amino}-3-methyl-2-oxo-2,3,4,5,6,7-hexahydro-1H-12,8-(metheno)-1,9-benzodiazacyclotetradecin-15-yl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Potent, Orally Bioavailable and Efficacious Macrocyclic Inhibitors of Factor XIa. Discovery of Pyridine-Based Macrocycles Possessing Phenylazole Carboxamide P1 Groups.

Corte, J.R.Pinto, D.J.P.Fang, T.Osuna, H.Yang, W.Wang, Y.Lai, A.Clark, C.Sun, J.H.Rampulla, R.A.Mathur, A.Kaspady, M.Neithnadka, P.R.Li, Y.X.Rossi, K.A.Myers, J.E.Sheriff, S.Lou, Z.Harper, T.W.Huang, C.S.Zheng, J.J.Bozarth, J.M.Wu, Y.Wong, P.C.Crain, E.Seiffert, D.A.Luettgen, J.M.Lam, P.Wexler, R.R.Ewing, W.R.

(2019) J.Med.Chem. 63: 784-803

  • DOI: 10.1021/acs.jmedchem.9b01768
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Factor XIa (FXIa) inhibitors are promising novel anticoagulants, which show excellent efficacy in preclinical thrombosis models with minimal effects on hemostasis. The discovery of potent and selective FXIa inhibitors which are also orally bioavailab ...

    Factor XIa (FXIa) inhibitors are promising novel anticoagulants, which show excellent efficacy in preclinical thrombosis models with minimal effects on hemostasis. The discovery of potent and selective FXIa inhibitors which are also orally bioavailable has been a challenge. Here, we describe optimization of the imidazole-based macrocyclic series and our initial progress toward meeting this challenge. A two-pronged strategy, which focused on replacement of the imidazole scaffold and the design of new P1 groups, led to the discovery of potent, orally bioavailable pyridine-based macrocyclic FXIa inhibitors. Moreover, pyridine-based macrocycle 19 , possessing the phenylimidazole carboxamide P1, exhibited excellent selectivity against relevant blood coagulation enzymes and displayed antithrombotic efficacy in a rabbit thrombosis model.


    Related Citations: 
    • 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 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
    • 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
    • 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
    • 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 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
    • 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
    • Orally Bioavailable Amine-Linked Macrocyclic Inhibitors of Factor XIa
      Fang, T.,Corte, J.R.,Gilligan, P.J.,Jeon, Y.,Osuna, H.,Rossi, K.A.,Myers, J.E., Jr.,Sheriff , S.,Lou, Z.,Zheng, J.J.,Harper, T.W.,Bozarth, J.M.,Wu, Y.,Luettgen, J.M.,Seiffert, D.A.,Wexler, R.R.,Lam, P.Y.S.
      () Bioorg. Med. Chem. Lett. --: --
    • 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
    • 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
    • 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 Research Center , Syngene International Pvt. Ltd. , Biocon Park, Plot No. 2 & 3, Bommasandra-Jigani Road , Bangalore 560 100 , India.,Research and Development , Bristol-Myers Squibb Company , 350 Carter Road , Hopewell , New Jersey 08540 , United States.,Research and Development , Bristol-Myers Squibb Company , US Rt. 206 & Province Line Road , Princeton , New Jersey 08540 , United States.,Research and Development , Bristol-Myers Squibb Company , 311 Pennington-Rocky Hill Road , Pennington , New Jersey 08543 , United States.




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
Coagulation factor XI
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
EDO
Query on EDO

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

Download SDF File 
Download CCD File 
A
methyl [(3R,7S)-7-{[1-(3-chloro-2-fluorophenyl)-5-methyl-1H-imidazole-4-carbonyl]amino}-3-methyl-2-oxo-2,3,4,5,6,7-hexahydro-1H-12,8-(metheno)-1,9-benzodiazacyclotetradecin-15-yl]carbamate
C31 H30 Cl F N6 O4
REWLFHBRHNXKCO-HXOBKFHXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.176 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.390α = 90.00
b = 79.390β = 90.00
c = 105.660γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-10-16 
  • Released Date: 2019-12-25 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-29
    Type: Data collection, Database references