5QQP

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(5E,8S)-8-[(4S)-4-(3-chlorophenyl)-2-oxopiperidin-1-yl]-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure based design of macrocyclic factor XIa inhibitors: Discovery of cyclic P1 linker moieties with improved oral bioavailability.

Clark, C.G.Rossi, K.A.Corte, J.R.Fang, T.Smallheer, J.M.De Lucca, I.Nirschl, D.S.Orwat, M.J.Pinto, D.J.P.Hu, Z.Wang, Y.Yang, W.Jeon, Y.Ewing, W.R.Myers Jr., J.E.Sheriff, S.Lou, Z.Bozarth, J.M.Wu, Y.Rendina, A.Harper, T.Zheng, J.Xin, B.Xiang, Q.Luettgen, J.M.Seiffert, D.A.Wexler, R.R.Lam, P.Y.S.

(2019) Bioorg Med Chem Lett 29: 126604-126604

  • DOI: https://doi.org/10.1016/j.bmcl.2019.08.008
  • Primary Citation of Related Structures:  
    5QQO, 5QQP

  • PubMed Abstract: 

    This manuscript describes the discovery of a series of macrocyclic inhibitors of FXIa with oral bioavailability. Assisted by structure based drug design and ligand bound X-ray crystal structures, the group linking the P1 moiety to the macrocyclic core was modified with the goal of reducing H-bond donors to improve pharmacokinetic performance versus 9. This effort resulted in the discovery of several cyclic P1 linkers, exemplified by 10, that are constrained mimics of the bioactive conformation displayed by the acrylamide linker of 9. These cyclic P1 linkers demonstrated enhanced bioavailability and improved potency.


  • Organizational Affiliation

    Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States. Electronic address: charles.clark@bms.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XI244Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NR7
Query on NR7

Download Ideal Coordinates CCD File 
B [auth A]methyl [(5E,8S)-8-[(4S)-4-(3-chlorophenyl)-2-oxopiperidin-1-yl]-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate
C29 H30 Cl N5 O4
YMEHWISYYMKMFO-WOMRJYOTSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NR7 BindingDB:  5QQP Ki: 5.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.91α = 90
b = 78.91β = 90
c = 105.73γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2019-09-18 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2021-05-12
    Changes: Structure summary
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary