3SOS

Benzothiazinone inhibitor in complex with FXIa

• PDB DOI: https://doi.org/10.2210/pdb3SOS/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2011-06-30 Released: 2012-04-11 
• Deposition Author(s): Fradera, X., Kazemier, B., Oubrie, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.278 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 

Literature

High-resolution crystal structures of factor XIa coagulation factor in complex with nonbasic high-affinity synthetic inhibitors.

Fradera, X., Kazemier, B., Carswell, E., Cooke, A., Oubrie, A., Hamilton, W., Dempster, M., Krapp, S., Nagel, S., Jestel, A.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 404-408

• PubMed: 22505407 
• DOI: https://doi.org/10.1107/S1744309112009037
• Primary Citation of Related Structures:  
  3SOR, 3SOS


• PubMed Abstract: 
  

  Factor XI (FXI) is a key enzyme in the coagulation pathway and an attractive target for the development of anticoagulant drugs. A small number of high-resolution crystal structures of FXIa in complex with small synthetic inhibitors have been published to date. All of these ligands have a basic P1 group and bind exclusively in the nonprime side of the active site of FXIa. Here, two structures of FXIa in complex with nonbasic inhibitors that occupy both the prime and nonprime sides of the active site are presented. These new structures could be valuable in the design and optimization of new FXIa synthethic inhibitors.

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Organizational Affiliation: 

Merck Research Laboratories, MSD, Newhouse, Lanarkshire ML1 5SH, Scotland. [e-mail]

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: 27.73 kDa 
• Atom Count: 2,059 
• Modelled Residue Count: 236 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XI	A	238	Homo sapiens	Mutation(s): 1  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
O61	D [auth A]	N-[(2S)-1-({2-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]ethyl}amino)-1-oxo-3-phenylpropan-2-yl]-3-oxo-3,4-dihydro-2H-1,4-benzothiazine-7-carboxamide C27 H24 Cl N7 O3 S IAXDWTLDVZYTHX-QFIPXVFZSA-N
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001115 (O61)	D [auth A]	N-[(2S)-1-({2-[5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL]ETHYL}AMINO)-1-OXO-3-PHENYLPROPAN-2-YL]-3-OXO-3,4-DIHYDRO-2H-1,4-BENZOTHIAZINE-7-CARBOXAMIDE	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.278 
• R-Value Work: 0.199 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.114	α = 90
b = 59.548	β = 90
c = 66.755	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Fradera, X., Kazemier, B., Oubrie, A.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2013-01-23
  Changes: Database references
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description