4X6N

FACTOR XIA IN COMPLEX WITH THE INHIBITOR 1-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-3-[5-chloro-2-(1H-tetrazol-1-yl)benzyl]urea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1635-1642

  • DOI: 10.1016/j.bmcl.2015.01.028
  • Primary Citation of Related Structures:  
  • Also Cited By: 4Y8Z, 4Y8Y, 4Y8X, 6C0S, 5QCN, 5QCM, 5QCL, 5QCK, 5Q0H, 5Q0G, 5Q0F, 5Q0E, 5Q0D, 5WB6, 5EXL

  • PubMed Abstract: 
  • Compound 2 was previously identified as a potent inhibitor of factor XIa lacking oral bioavailability. A structure-based approach was used to design analogs of 2 with novel P1 moieties with good selectivity profiles and oral bioavailability. Further ...

    Compound 2 was previously identified as a potent inhibitor of factor XIa lacking oral bioavailability. A structure-based approach was used to design analogs of 2 with novel P1 moieties with good selectivity profiles and oral bioavailability. Further optimization of the P1 group led to the identification of a 4-chlorophenyltetrazole P1 analog, which when combined with further modifications to the linker and P2' group provided compound 32 with FXIa Ki=6.7 nM and modest oral exposure in dogs.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Bristol-Myers Squibb Company, Research and Development, 311 Pennington-Rocky Hill Rd., Pennington, NJ 08534, United States. Electronic address: donald.pinto@bms.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XI, light chain
A
244Homo sapiensMutation(s): 2 
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
cleaved peptide
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
3Y5
Query on 3Y5

Download SDF File 
Download CCD File 
A
1-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-3-[5-chloro-2-(1H-tetrazol-1-yl)benzyl]urea
C27 H23 Cl2 N11 O
LCVIWSIVTGTOCS-NRFANRHFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3Y5Ki: 1.5 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.100α = 90.00
b = 79.100β = 90.00
c = 105.900γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-12-08 
  • Released Date: 2015-02-18 
  • Deposition Author(s): Wei, A.

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-03-18
    Type: Database references
  • Version 1.2: 2015-04-01
    Type: Database references