4NA8 | pdb_00004na8

Factor XIa in complex with the inhibitor 5-aminocarbonyl-2-[3-[(2s,4r)-6-carbamimidoyl-4-methyl-4-phenyl-2,3-dihydro-1h-quinolin-2-yl]phenyl]benzoic acid

• PDB DOI: https://doi.org/10.2210/pdb4NA8/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-21 Released: 2014-02-12 
• Deposition Author(s): Wei, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.271 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Tetrahydroquinoline Derivatives as Potent and Selective Factor XIa Inhibitors.

Quan, M.L., Wong, P.C., Wang, C., Woerner, F., Smallheer, J.M., Barbera, F.A., Bozarth, J.M., Brown, R.L., Harpel, M.R., Luettgen, J.M., Morin, P.E., Peterson, T., Ramamurthy, V., Rendina, A.R., Rossi, K.A., Watson, C.A., Wei, A., Zhang, G., Seiffert, D., Wexler, R.R.

(2014) J Med Chem 57: 955-969

• PubMed: 24405333 
• DOI: https://doi.org/10.1021/jm401670x
• Primary Citation Related Structures: 
  4NA7, 4NA8, 4NA9


• PubMed Abstract: 
  

  Antithrombotic agents that are inhibitors of factor XIa (FXIa) have the potential to demonstrate robust efficacy with a low bleeding risk profile. Herein, we describe a series of tetrahydroquinoline (THQ) derivatives as FXIa inhibitors. Compound 1 was identified as a potent and selective tool compound for proof of concept studies. It exhibited excellent antithrombotic efficacy in rabbit thrombosis models and did not prolong bleeding times. This demonstrates proof of concept for the FXIa mechanism in animal models with a reversible, small molecule inhibitor.

---

Organizational Affiliation: 
• Discovery Chemistry and Cardiovascular Biology, Research and Development, Bristol-Myers Squibb Company , 311 Pennington-Rocky Hill Road, Pennington, 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: 28.43 kDa 
• Atom Count: 2,011 
• Modeled Residue Count: 238 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XI	A	244	Homo sapiens	Mutation(s): 0  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
1T6	B [auth A]	5-aminocarbonyl-2-[3-[(2S,4R)-6-carbamimidoyl-4-methyl-4-phenyl-2,3-dihydro-1H-quinolin-2-yl]phenyl]benzoic acid C31 H28 N4 O3 DPAVVGLNAXECAW-JTSJOTPCSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.271 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.05	α = 90
b = 79.05	β = 90
c = 106.91	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Wei, A.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary