5QTW | pdb_00005qtw

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl (2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-14-[(methoxycarbonyl)amino]-2,3,4,5,6,7-hexahydro-1H-8,11-epimino-1,9-benzodiazacyclotridecine-2-carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.248 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5QTW

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Orally bioavailable amine-linked macrocyclic inhibitors of factor XIa.

Fang, T.Corte, J.R.Gilligan, P.J.Jeon, Y.Osuna, H.Rossi, K.A.Myers Jr., J.E.Sheriff, S.Lou, Z.Zheng, J.J.Harper, T.W.Bozarth, J.M.Wu, Y.Luettgen, J.M.Seiffert, D.A.Wexler, R.R.Lam, P.Y.S.

(2020) Bioorg Med Chem Lett 30: 126949-126949

  • DOI: https://doi.org/10.1016/j.bmcl.2020.126949
  • Primary Citation Related Structures: 
    5QTV, 5QTW, 5QTX, 5QTY

  • PubMed Abstract: 

    The discovery of orally bioavailable FXIa inhibitors has been a challenge. Herein, we describe our efforts to address this challenge by optimization of our imidazole-based macrocyclic series. Our optimization strategy focused on modifications to the P2 prime, macrocyclic amide linker, and the imidazole scaffold. Replacing the amide of the macrocyclic linker with amide isosteres led to the discovery of substituted amine linkers which not only maintained FXIa binding affinity but also improved oral exposure in rats. Combining the optimized macrocyclic amine linker with a pyridine scaffold afforded compounds 23 and 24 that were orally bioavailable, single-digit nanomolar FXIa inhibitors with excellent selectivity against relevant blood coagulation enzymes.


  • Organizational Affiliation
    • Bristol-Myers Squibb Company, Research and Development, 350 Carter Road, Hopewell, NJ 08540, United States. Electronic address: tianan.fang@bms.com.

Macromolecule Content 

  • Total Structure Weight: 29.28 kDa 
  • Atom Count: 2,151 
  • 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
QLM

Query on QLM



Download:Ideal Coordinates CCD File
B [auth A]methyl (2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-14-[(methoxycarbonyl)amino]-2,3,4,5,6,7-hexahydro-1H-8,11-epimino-1,9-benzodiazacyclotridecine-2-carboxylate
C29 H30 Cl N9 O5
IMAMZDHZESKXTJ-VFPWRSFOSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.248 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.8α = 90
b = 78.8β = 90
c = 105.8γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-01-29 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Database references
  • Version 1.2: 2020-03-18
    Changes: Data collection, Database references
  • Version 1.3: 2021-05-12
    Changes: Structure summary
  • Version 1.4: 2024-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2026-02-18
    Changes: Refinement description