5QTU | pdb_00005qtu

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(3R,7S)-7-{[1-(3-chloro-2-fluorophenyl)-5-methyl-1H-imidazole-4-carbonyl]amino}-3-methyl-2-oxo-2,3,4,5,6,7-hexahydro-1H-12,8-(metheno)-1,9-benzodiazacyclotetradecin-15-yl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 
    0.236 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5QTU

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Potent, Orally Bioavailable and Efficacious Macrocyclic Inhibitors of Factor XIa. Discovery of Pyridine-Based Macrocycles Possessing Phenylazole Carboxamide P1 Groups.

Corte, J.R.Pinto, D.J.P.Fang, T.Osuna, H.Yang, W.Wang, Y.Lai, A.Clark, C.Sun, J.H.Rampulla, R.A.Mathur, A.Kaspady, M.Neithnadka, P.R.Li, Y.X.Rossi, K.A.Myers, J.E.Sheriff, S.Lou, Z.Harper, T.W.Huang, C.S.Zheng, J.J.Bozarth, J.M.Wu, Y.Wong, P.C.Crain, E.Seiffert, D.A.Luettgen, J.M.Lam, P.Wexler, R.R.Ewing, W.R.

(2019) J Med Chem 63: 784-803

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01768
  • Primary Citation Related Structures: 
    5QTT, 5QTU

  • PubMed Abstract: 

    Factor XIa (FXIa) inhibitors are promising novel anticoagulants, which show excellent efficacy in preclinical thrombosis models with minimal effects on hemostasis. The discovery of potent and selective FXIa inhibitors which are also orally bioavailable has been a challenge. Here, we describe optimization of the imidazole-based macrocyclic series and our initial progress toward meeting this challenge. A two-pronged strategy, which focused on replacement of the imidazole scaffold and the design of new P1 groups, led to the discovery of potent, orally bioavailable pyridine-based macrocyclic FXIa inhibitors. Moreover, pyridine-based macrocycle 19 , possessing the phenylimidazole carboxamide P1, exhibited excellent selectivity against relevant blood coagulation enzymes and displayed antithrombotic efficacy in a rabbit thrombosis model.


  • Organizational Affiliation
    • Research and Development , Bristol-Myers Squibb Company , 350 Carter Road , Hopewell , New Jersey 08540 , United States.

Macromolecule Content 

  • Total Structure Weight: 31.02 kDa 
  • Atom Count: 2,084 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 262 
  • Unique protein chains: 2

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
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor XIB [auth H]18Homo 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
QEV
(Subject of Investigation/LOI)

Query on QEV



Download:Ideal Coordinates CCD File
C [auth A]methyl [(3R,7S)-7-{[1-(3-chloro-2-fluorophenyl)-5-methyl-1H-imidazole-4-carbonyl]amino}-3-methyl-2-oxo-2,3,4,5,6,7-hexahydro-1H-12,8-(metheno)-1,9-benzodiazacyclotetradecin-15-yl]carbamate
C31 H30 Cl F N6 O4
REWLFHBRHNXKCO-HXOBKFHXSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
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]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.39α = 90
b = 79.39β = 90
c = 105.66γ = 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: 2019-12-25 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Database references
  • Version 1.2: 2021-05-12
    Changes: Database references, Structure summary
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2026-02-18
    Changes: Refinement description