6W50

FACTOR XIA IN COMPLEX WITH THE INHIBITOR METHYL ((10R,14S)- 14-(4-(3-CHLORO-2,6-DIFLUOROPHENYL)-6-OXO-3,6-DIHYDRO- 1(2H)-PYRIDINYL)-10-METHYL-9-OXO-8,16- DIAZATRICYCLO[13.3.1.0~2,7~]NONADECA-1(19),2,4,6,15,17- HEXAEN-5-YL)CARBAMATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of a High Affinity, Orally Bioavailable Macrocyclic FXIa Inhibitor with Antithrombotic Activity in Preclinical Species.

Yang, W.Wang, Y.Lai, A.Clark, C.G.Corte, J.R.Fang, T.Gilligan, P.J.Jeon, Y.Pabbisetty, K.B.Rampulla, R.A.Mathur, A.Kaspady, M.Neithnadka, P.R.Arumugam, A.Raju, S.Rossi, K.A.Myers Jr., J.E.Sheriff, S.Lou, Z.Zheng, J.J.Chacko, S.A.Bozarth, J.M.Wu, Y.Crain, E.J.Wong, P.C.Seiffert, D.A.Luettgen, J.M.Lam, P.Y.S.Wexler, R.R.Ewing, W.R.

(2020) J Med Chem 63: 7226-7242

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00464
  • Primary Citation of Related Structures:  
    6W50

  • PubMed Abstract: 

    Oral factor XIa (FXIa) inhibitors may provide a promising new antithrombotic therapy with an improved benefit to bleeding risk profile over existing antithrombotic agents. Herein, we report application of a previously disclosed cyclic carbamate P1 linker which provided improved oral bioavailability in the imidazole-based 13-membered macrocycle to the 12-membered macrocycle. This resulted in identification of compound 4 with desired FXIa inhibitory potency and good oral bioavailability but high in vivo clearance. Further structure-activity relationship (SAR) studies of heterocyclic core modifications to replace the imidazole core as well as various linkers to the P1 group led to the discovery of compound 6f , a potent FXIa inhibitor with selectivity against most of the relevant serine proteases. Compound 6f also demonstrated excellent pharmacokinetics (PK) profile (high oral bioavailability and low clearance) in multiple preclinical species. Compound 6f achieved robust antithrombotic efficacy in a rabbit efficacy model at doses which preserved hemostasis.


  • Organizational Affiliation

    Research and Development, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08540, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XI244Homo sapiensMutation(s): 2 
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
GTEx:  ENSG00000088926 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SWP (Subject of Investigation/LOI)
Query on SWP

Download Ideal Coordinates CCD File 
B [auth A]methyl ((10R,14S)-14-(4-(3-chloro-2,6-difluorophenyl)-6-oxo-3,6-dihydro- 1(2h)-pyridinyl)-10-methyl-9-oxo-8,16-diazatricyclo[13.3.1.0~2,7~]nonadeca- 1(19),2,4,6,15,17-hexaen-5-yl)carbamate
C31 H29 Cl F2 N4 O4
AXXYATYQRMPQSN-QUGAMOGWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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],
N [auth A],
O [auth A],
P [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SWP BindingDB:  6W50 Ki: 0.26 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.86α = 90
b = 78.86β = 90
c = 106.62γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
AMoREphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-06-10 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary