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 

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

  • 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.

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin
A
289Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hirudin IIIB'
B
10Hirudo medicinalisMutation(s): 0 
Find proteins for P28511 (Hirudo medicinalis)
Go to UniProtKB:  P28511
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
UNB
Query on UNB
Download SDF File 
Download CCD File 
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UNBIC50: 17 nM BINDINGMOAD
UNBIC50: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.918α = 90.00
b = 71.649β = 99.56
c = 71.234γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CCP4data scaling
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


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 

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