5QQP | pdb_00005qqp

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 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5QQP

Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 28.74 kDa 
  • Atom Count: 2,143 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 244 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.190 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
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
  • Version 1.4: 2026-02-18
    Changes: Refinement description