4Y8X

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

• PDB DOI: https://doi.org/10.2210/pdb4Y8X/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-02-16 Released: 2015-05-27 
• Deposition Author(s): Sheriff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.164 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 

Starting Model: experimental

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 
• 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.

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Organizational Affiliation: 

Research and Development, Bristol-Myers Squibb , Princeton, New Jersey 08543, United States.

Biological Assembly 1  

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

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

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XIa	A	244	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4GR	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	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	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 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.78	α = 90
b = 78.78	β = 90
c = 106.32	γ = 120

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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