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 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  
    5QTT, 5QTU

  • 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 bioavailable has been a challenge ...

    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: 
    • 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., 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
    • 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 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 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 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
    • 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
    • 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
    • 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 Jr., J.E., 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.
      (2020) Bioorg Med Chem Lett 30: 126949

    Organizational Affiliation

    Research and Development , Bristol-Myers Squibb Company , 350 Carter Road , Hopewell , New Jersey 08540 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIA244Homo sapiensMutation(s): 0 
Gene Names: F11
EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
PHAROS:  P03951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIB [auth H]18Homo sapiensMutation(s): 0 
Gene Names: F11
EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
PHAROS:  P03951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QEV (Subject of Investigation/LOI)
Query on QEV

Download Ideal Coordinates CCD File 
C [auth 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
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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 
  • R-Value Observed: 0.177 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.39α = 90
b = 79.39β = 90
c = 105.66γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Database references
  • Version 1.2: 2021-05-12
    Changes: Database references, Structure summary