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 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5EXM, 5EXL, 5EXN

  • 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
    • 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.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
    • 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 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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIa light chainA238Homo sapiensMutation(s): 1 
Gene Names: F11
EC: 3.4.21.27
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
NIH Common Fund Data Resources
PHAROS  P03951
GTEx  ENSG00000088926
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5SU
Query on 5SU
Download Ideal Coordinates 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 Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5SUKi:  23   nM  Binding MOAD
5SUKi:  23   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.89α = 90
b = 69.12β = 90
c = 85.32γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
AMoREphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

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
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary