4Y8X | pdb_00004y8x

Factor XIa in complex with the inhibitor methyl (4-{4-chloro-2-[(1S)-1-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-2-phenylethyl]-1H-imidazol-5-yl}phenyl)carbamate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.164 (Depositor), 0.162 (DCC) 
  • R-Value Work: 
    0.158 (Depositor) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

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: 590-595

  • DOI: https://doi.org/10.1021/acsmedchemlett.5b00066
  • Primary Citation Related Structures: 
    4Y8X, 4Y8Y, 4Y8Z

  • PubMed Abstract: 

    Structure-activity relationship optimization of phenylalanine P1' and P2' regions with a phenylimidazole core resulted in a series of potent FXIa inhibitors. Introducing 4-hydroxyquinolin-2-one as the P2' group enhanced FXIa affinity and metabolic stability. Incorporation of an N-methyl piperazine amide group to replace the phenylalanine improved both FXIa potency and aqueous solubility. Combination of the optimization led to the discovery of FXIa inhibitor 13 with a FXIa K i of 0.04 nM and an aPTT EC2x of 1.0 μM. Dose-dependent efficacy (EC50 of 0.53 μM) was achieved in the rabbit ECAT model with minimal bleeding time prolongation.

    • Organizational Affiliation: 
    • Research and Development, Bristol-Myers Squibb , Princeton, New Jersey 08543, United States.

Macromolecule Content 

  • Total Structure Weight: 28.95 kDa 
  • Atom Count: 2,177 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 244 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor XIa244Homo 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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4GR

Query on 4GR


Download:Ideal Coordinates CCD File
B [auth A]methyl (4-{4-chloro-2-[(1S)-1-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-2-phenylethyl]-1H-imidazol-5-yl}phenyl)carbamate
C29 H24 Cl2 N8 O3
GLCBWRQIUCCILC-PZVJUEDKSA-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]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.164 (Depositor), 0.162 (DCC) 
  • R-Value Work:  0.158 (Depositor) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.78α = 90
b = 78.78β = 90
c = 106.32γ = 120
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2015-05-27 
    • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2024-11-06
    Changes: Structure summary