4WXI | pdb_00004wxi

FACTOR XIA IN COMPLEX WITH THE INHIBITOR trans-N-{(1S)-1-[4-(3-amino-2H-indazol-6-yl)pyridin-2-yl]-2-phenylethyl}-4-(aminomethyl)cyclohexanecarboxamide

• PDB DOI: https://doi.org/10.2210/pdb4WXI/pdb

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


• Deposited: 2014-11-13 Released: 2015-01-28 
• Deposition Author(s): Wei, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Pyridine and pyridinone-based factor XIa inhibitors.

Corte, J.R., Fang, T., Hangeland, J.J., Friends, T.J., Rendina, A.R., Luettgen, J.M., Bozarth, J.M., Barbera, F.A., Rossi, K.A., Wei, A., Ramamurthy, V., Morin, P.E., Seiffert, D.A., Wexler, R.R., Quan, M.L.

(2015) Bioorg Med Chem Lett 25: 925-930

• PubMed: 25592713 
• DOI: https://doi.org/10.1016/j.bmcl.2014.12.050
• Primary Citation Related Structures: 
  4WXI


• PubMed Abstract: 
  

  The structure-activity relationships (SAR) of six-membered ring replacements for the imidazole ring scaffold is described. This work led to the discovery of the potent and selective pyridine (S)-23 and pyridinone (±)-24 factor XIa inhibitors. SAR and X-ray crystal structure data highlight the key differences between imidazole and six-membered ring analogs.

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Organizational Affiliation: 
• Discovery Chemistry and Cardiovascular Biology, Research and Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky Hill Road, Pennington, NJ 08543, United States. Electronic address: [e-mail].
Discovery Chemistry and Cardiovascular Biology, Research and Development, Bristol-Myers Squibb Company, 311 Pennington-Rocky Hill Road, Pennington, NJ 08543, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.39 kDa 
• Atom Count: 2,054 
• 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, LIGHT CHAIN	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
3VM	B [auth A]	trans-N-{(1S)-1-[4-(3-amino-2H-indazol-6-yl)pyridin-2-yl]-2-phenylethyl}-4-(aminomethyl)cyclohexanecarboxamide C28 H32 N6 O ABPMTNUZKFZRKL-DYLHXGEVSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79	α = 90
b = 79	β = 90
c = 106.5	γ = 120

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Wei, A.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Database references
• Version 1.2: 2015-02-18
  Changes: Database references
• Version 1.3: 2018-08-29
  Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Refinement description, Structure summary