6ROT

Thrombin in complex with MI2105


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.339 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.

Sandner, A.Hufner-Wulsdorf, T.Heine, A.Steinmetzer, T.Klebe, G.

(2019) J.Med.Chem. 62: 9753-9771

  • DOI: 10.1021/acs.jmedchem.9b01196
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation ...

    Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation in solution and complex formation have been characterized by crystallography, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations. First, we show why these preorganizing modifications do not affect the overall binding mode and how key interactions are preserved. Next, we demonstrate how preorganization thermodynamics can be largely dominated by enthalpy rather than entropy because of the significant population of low-energy conformations. Furthermore, a salt bridge is shielded by actively reducing its surface exposure, thus leading to an enhanced enthalpic binding profile. Our results suggest that the consideration of the ligand solution ensemble by MD simulation is necessary to predict preorganizing modifications that enhance the binding behavior of already promising binders.


    Organizational Affiliation

    Institut für Pharmazeutische Chemie , Philipps-Universität Marburg , Marbacher Weg 6 , 35032 Marburg , 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 Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
H
253Homo 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: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin variant-2
A
12Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
H
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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H
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
KDQ
Query on KDQ

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Download CCD File 
H
(2~{S})-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]-1-[2-[(phenylmethyl)sulfonylamino]ethanoyl]pyrrolidine-2-carboxamide
C22 H26 Cl N3 O5 S
ZWZCPMJCUATTCO-FQEVSTJZSA-N
 Ligand Interaction
NAG
Query on NAG

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H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
A
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.339 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.137 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.926α = 90.00
b = 71.177β = 100.72
c = 73.006γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHASERphasing
PHENIXrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release