5Q0E

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(4S,8S)-8-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-4-methyl-2-oxo-1,3,4,5,6,7,8,10-octahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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, 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: 3833-3839

  • DOI: 10.1016/j.bmcl.2017.06.058
  • Primary Citation of Related Structures:  
  • Also Cited By: 5QTU, 5QTT, 5QQP, 5QQO, 6C0S, 5QCN, 5QCM, 5QCL, 5QCK, 5WB6

  • PubMed Abstract: 
  • Optimization of macrocyclic inhibitors of FXIa is described which focused on modifications to both the macrocyclic linker and the P1 group. Increases in potency were discovered through interactions with a key hydrophobic region near the S1 prime pock ...

    Optimization of macrocyclic inhibitors of FXIa is described which focused on modifications to both the macrocyclic linker and the P1 group. Increases in potency were discovered through interactions with a key hydrophobic region near the S1 prime pocket by substitution of the macrocyclic linker with small alkyl groups. Both the position of substitution and the absolute stereochemistry of the alkyl groups on the macrocyclic linker which led to improved potency varied depending on the ring size of the macrocycle. Replacement of the chlorophenyltetrazole cinnamide P1 in these optimized macrocycles reduced the polar surface area and improved the oral bioavailability for the series, albeit at the cost of a decrease in potency.


    Related Citations: 
    • 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, 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
    • 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, 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
    • 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, L.M.,Rossi, K.A.,Rendina, A.R.,Bozarth, J.M.,Zhang, G.,Wei, A.,Ramamurthy, V.,Sheriff, S.,Myers, J.E.,Morin, P.E.,Luettgen, J.M.,Seiffert, D.A.,Quan, M.L.,Wexler, R.R.
      (2015) Bioorg. Med. Chem. Lett. 25: 1635
    • 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
    • Novel phenylalanine derived diamides as Factor XIa inhibitors.
      Smith, 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.,Wexler, R.R.,Pinto, D.J.
      (2016) Bioorg. Med. Chem. Lett. 26: 472
    • 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, 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


    Organizational Affiliation

    Bristol-Myers Squibb Company, Research and Development, 350 Carter Road, Hopewell, NJ 08540, United States. Electronic address: james.corte@bms.com.,Bristol-Myers Squibb Company, Research and Development, 311 Pennington-Rocky Hill Road, Pennington, NJ 08543-2130, United States.,Bristol-Myers Squibb Company, Research and Development, 350 Carter Road, Hopewell, NJ 08540, United States.,Bristol-Myers Squibb Company, Research and Development, US Rt. 206 & Province Line Road, Princeton, NJ 08540, United States.,Bristol-Myers Squibb Company, Research and Development, 350 Carter Road, Hopewell, NJ 08540, United States. Electronic address: wu.yang@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
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
9FD
Query on 9FD

Download SDF File 
Download CCD File 
A
methyl [(4S,8S)-8-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-4-methyl-2-oxo-1,3,4,5,6,7,8,10-octahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate
C29 H30 Cl N9 O4
GTMMYYLRFTWUSN-GQTIVUJGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9FDKi: 0.69 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.173 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.800α = 90.00
b = 78.800β = 90.00
c = 106.000γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
AMoREphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-05-01 
  • Released Date: 2017-07-12 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references
  • Version 1.2: 2018-02-21
    Type: Structure summary