FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl (4-{4-chloro-2-[(1S)-1-({3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]propanoyl}amino)-2-phenylethyl]-1H-imidazol-5-yl}phenyl)carbamate

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1016/j.bmcl.2015.01.028
  • Primary Citation of Related Structures:  
    4X6M, 4X6N, 4X6O, 4X6P

  • 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 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.

  • 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XI, light chain244Homo sapiensMutation(s): 2 
Gene Names: F11
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
PHAROS:  P03951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3Y4

Download Ideal Coordinates CCD File 
B [auth A]methyl (4-{4-chloro-2-[(1S)-1-({3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]propanoyl}amino)-2-phenylethyl]-1H-imidazol-5-yl}phenyl)carbamate
C29 H26 Cl2 N8 O3
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
O4 S
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]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
3Y4 Binding MOAD:  4X6O Ki: 1.9 (nM) from 1 assay(s)
BindingDB:  4X6O IC50: 3.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.7α = 90
b = 78.7β = 90
c = 106.3γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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