Factor XIa in complex with compound 11

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 

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Augmenting Hit Identification by Virtual Screening Techniques in Small Molecule Drug Discovery.

Yan, X.C.Sanders, J.M.Gao, Y.D.Tudor, M.Haidle, A.M.Klein, D.J.Converso, A.Lesburg, C.A.Zang, Y.Wood, H.B.

(2020) J Chem Inf Model 60: 4144-4152

  • DOI: https://doi.org/10.1021/acs.jcim.0c00113
  • Primary Citation of Related Structures:  
    6VLM, 6VLU, 6VLV

  • PubMed Abstract: 

    Two orthogonal approaches for hit identification in drug discovery are large-scale in vitro and in silico screening. In recent years, due to the emergence of new targets and a rapid increase in the size of the readily synthesizable chemical space, there is a growing emphasis on the integration of the two techniques to improve the hit finding efficiency. Here, we highlight three examples of drug discovery projects at Merck & Co., Inc., Kenilworth, NJ, USA in which different virtual screening (VS) techniques, each specifically tailored to leverage knowledge available for the target, were utilized to augment the selection of high-quality chemical matter for in vitro assays and to enhance the diversity and tractability of hits. Central to success is a fully integrated workflow combining in silico and experimental expertise at every stage of the hit identification process. We advocate that workflows encompassing VS as part of an integrated hit finding plan should be widely adopted to accelerate hit identification and foster cross-functional collaborations in modern drug discovery.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor XIa light chain238Homo sapiensMutation(s): 1 
Gene Names: F11
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
GTEx:  ENSG00000088926 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R3A (Subject of Investigation/LOI)
Query on R3A

Download Ideal Coordinates CCD File 
D [auth A]1-carbamimidamido-4-chloro-N-[(2R)-3-methyl-1-(morpholin-4-yl)-1-oxobutan-2-yl]isoquinoline-7-sulfonamide
C19 H25 Cl N6 O4 S
Query on FLC

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C6 H5 O7
Binding Affinity Annotations 
IDSourceBinding Affinity
R3A Binding MOAD:  6VLV Ki: 5.33 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.23α = 90
b = 59.88β = 90
c = 67.9γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references