1K21

HUMAN THROMBIN-INHIBITOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.

Dullweber, F.Stubbs, M.T.Musil, D.Sturzebecher, J.Klebe, G.

(2001) J Mol Biol 313: 593-614

  • DOI: 10.1006/jmbi.2001.5062
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The binding of a series of low molecular weight ligands towards trypsin and thrombin has been studied by isothermal titration calorimetry and protein crystallography. In a series of congeneric ligands, surprising changes of protonation states occur a ...

    The binding of a series of low molecular weight ligands towards trypsin and thrombin has been studied by isothermal titration calorimetry and protein crystallography. In a series of congeneric ligands, surprising changes of protonation states occur and are overlaid on the binding process. They result from induced pK(a) shifts depending on the local environment experienced by the ligand and protein functional groups in the complex (induced dielectric fit). They involve additional heat effects that must be corrected before any conclusion on the binding enthalpy (DeltaH) and entropy (DeltaS) can be drawn. After correction, trends in both contributions can be interpreted in structural terms with respect to the hydrogen bond inventory or residual ligand motions. For all inhibitors studied, a strong negative heat capacity change (DeltaC(p)) is detected, thus binding becomes more exothermic and entropically less favourable with increasing temperature. Due to a mutual compensation, Gibbs free energy remains virtually unchanged. The strong negative DeltaC(p) value cannot solely be explained by the removal of hydrophobic surface portions of the protein or ligand from water exposure. Additional contributions must be considered, presumably arising from modulations of the local water structure, changes in vibrational modes or other ordering parameters. For thrombin, smaller negative DeltaC(p) values are observed for ligand binding in the presence of sodium ions compared to the other alkali ions, probably due to stabilising effects on the protein or changes in the bound water structure.


    Related Citations: 
    • Structural and Functional Analyses of Benzamidine-Based Inhibitors in Complex with Trypsin: Implications for the Inhibition of Factor Xa, Tpa, and Urokinase
      Renatus, M., Bode, W., Huber, R., Stuerzebecher, J., Stubbs, M.T.
      (1998) J Med Chem 41: 5445
    • Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin
      Stubbs, M.T., Huber, R., Bode, W.
      (1995) FEBS Lett 375: 103
    • A Player of Many Parts: The Spotlight Falls on Thrombin'S Structure
      Stubbs, M.T., Bode, W.
      (1993) Thromb Res 69: 1

    Organizational Affiliation

    Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg (Lahn), Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin variant-2
I
12Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IGN
Query on IGN

Download CCD File 
H
{[(1R)-2-((2S)-2-{[(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)AMINO]CARBONYL}PIPERIDINYL)-1-(CYCLOHEXYLMETHYL)-2-OXOETHYL]AMINO}ACETIC ACID
C21 H38 N6 O4
CDPROXZBMHOBTQ-SJORKVTESA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
IL-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IGNIC50:  22400   nM  BindingDB
IGNKi:  4.199999809265137   nM  Binding MOAD
IGNIC50:  1300   nM  BindingDB
IGNKi :  4.199999809265137   nM  PDBBind
IGNIC50:  17   nM  BindingDB
IGNKi:  3   nM  BindingDB
IGNKi:  15   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.619α = 90
b = 71.546β = 100.12
c = 71.821γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-08
    Type: Initial release
  • Version 1.1: 2007-10-16
    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