5EXN | pdb_00005exn

FACTOR XIA (C500S [C122S]) IN COMPLEX WITH THE INHIBITOR methyl ~{N}-[4-[2-[(1~{S})-1-[[(~{E})-3-[5-chloranyl-2-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]amino]-2-phenyl-ethyl]pyridin-4-yl]phenyl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5EXN

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Orally bioavailable pyridine and pyrimidine-based Factor XIa inhibitors: Discovery of the methyl N-phenyl carbamate P2 prime group

Corte, J.R.Fang, T.Pinto, D.J.P.Orwat, M.J.Han, W.Rendina, A.R.Luettgen, J.M.Rossi, K.A.Wei, A.Ramamurthy, V.Myers Jr., J.E.Sheriff, S.Narayanan, R.Harper, T.Zheng, J.J.Li, Y.-X.Seiffert, D.A.Wexler, R.R.Quan, M.L.

(2016) Bioorg Med Chem 24: 2257-2272

  • DOI: https://doi.org/10.1016/j.bmc.2016.03.062
  • Primary Citation Related Structures: 
    5EXL, 5EXM, 5EXN

  • PubMed Abstract: 

    Pyridine-based Factor XIa (FXIa) inhibitor (S)-2 was optimized by modifying the P2 prime, P1, and scaffold regions. This work resulted in the discovery of the methyl N-phenyl carbamate P2 prime group which maintained FXIa activity, reduced the number of H-bond donors, and improved the physicochemical properties compared to the amino indazole P2 prime moiety. Compound (S)-17 was identified as a potent and selective FXIa inhibitor that was orally bioavailable. Replacement of the basic cyclohexyl methyl amine P1 in (S)-17 with the neutral p-chlorophenyltetrazole P1 resulted in the discovery of (S)-24 which showed a significant improvement in oral bioavailability compared to the previously reported imidazole (S)-23. Additional improvements in FXIa binding affinity, while maintaining oral bioavailability, was achieved by replacing the pyridine scaffold with either a regioisomeric pyridine or pyrimidine ring system.


  • Organizational Affiliation
    • Bristol-Myers Squibb Company, Research and Development, P.O. Box 5400, Princeton, NJ 08543, United States. Electronic address: james.corte@bms.com.

Macromolecule Content 

  • Total Structure Weight: 27.66 kDa 
  • Atom Count: 2,142 
  • Modeled Residue Count: 237 
  • Deposited Residue Count: 238 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor XIa light chain238Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P03951-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5SU

Query on 5SU



Download:Ideal Coordinates CCD File
C [auth A]methyl ~{N}-[4-[2-[(1~{S})-1-[[(~{E})-3-[5-chloranyl-2-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]amino]-2-phenyl-ethyl]pyridin-4-yl]phenyl]carbamate
C31 H26 Cl N7 O3
ZBUQQUJRHVSUJI-CWBDRXANSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.89α = 90
b = 69.12β = 90
c = 85.32γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-04-13 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Structure summary