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: 2.00 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  
    5QQP, 5QQO

  • 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 core was modified with the goal of reducing H-bond donors to improve pharmacokinetic performance versus 9 ...

    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: 
    • 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
    • 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

    Organizational Affiliation

    Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MET-ASP-ASP-ASP-ASP-LYS-MET-ASP-ASN-GLU-CYS-THR-THR-LYS-ILE-LYS-PRO-ARGB [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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NRJ (Subject of Investigation/LOI)
Query on NRJ

Download Ideal Coordinates CCD File 
C [auth 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
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] , J [auth A] , K [auth A] , L [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],  N [auth A],  O [auth A],  P [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NRJ Binding MOAD:  5QQO Ki: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.86α = 90
b = 78.86β = 90
c = 106.01γ = 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

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2021-05-12
    Changes: Structure summary