2BDY

thrombin in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure.

Hanessian, S., Therrien, E., van Otterlo, W.A., Bayrakdarian, M., Nilsson, I., Xue, Y.

(2006) Bioorg Med Chem Lett 16: 1032-1036

  • DOI: 10.1016/j.bmcl.2005.10.082
  • Primary Citation of Related Structures:  
    2BDY

  • PubMed Abstract: 

    • Prototypical thrombin inhibitors were synthesized based on a trisubstituted phenol as a core motif. A naphthylsulfonamide analogue showed excellent antithrombin activity. An X-ray co-crystal structure showed the expected interactions.

    Organizational Affiliation: 

    Department of Chemistry, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, PQ, Canada H3C 3J7. stephen.hanessian@umontreal.ca



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ThrombinA289Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hirudin IIIB'B10Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P01050 (Hirudo medicinalis)
Explore P01050 
Go to UniProtKB:  P01050
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01050
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNB
Query on UNB
Download Ideal Coordinates CCD File 
D [auth A]N-(4-CARBAMIMIDOYL-BENZYL)-2-[2-HYDROXY-6-METHYL-3-(NAPHTHALENE-1-SULFONYLAMINO)-PHENYL]-ACETAMIDE
C27 H26 N4 O4 S
KWJVADNYZMUTJY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS		B L-PEPTIDE LINKINGC9 H11 N O6 STYR
Binding Affinity Annotations 
IDSourceBinding Affinity
UNB PDBBind:  2BDY IC50: 17 (nM) from 1 assay(s)
BindingDB:  2BDY IC50: 17 (nM) from 1 assay(s)
Binding MOAD:  2BDY IC50: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.918α = 90
b = 71.649β = 99.56
c = 71.234γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2005-10-21 
  • Released Date: 2006-10-24 
    • Deposition Author(s): Xue, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2013-03-13
    Changes: Other
  • Version 1.5: 2017-10-18
    Changes: Refinement description