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Computed Structure Models (CSM)
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 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), 0.160 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model:experimental
View more details

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 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

  • PubMed: 26005539 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1021/acsmedchemlett.5b00066
  • Primary Citation of 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.
Biological Assembly 1  

 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (4GR)

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

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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
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • 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), 0.160 (DCC) 
  • R-Value Work: 0.158 (Depositor), 0.150 (DCC) 
  • 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

View Full Validation Report



Ligand Structure Quality Assessment 


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
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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