5AF9

Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report



Literature

Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.

Ruehmann, E.Betz, M.Heine, A.Klebe, G.

(2015) J Med Chem 58: 6960

  • DOI: 10.1021/acs.jmedchem.5b00812
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In lead optimization, small, enthalpically advantaged fragments have been suggested to be superior, as an entropic component will be added inevitably during late-stage optimization. Determination of thermodynamic signatures of weak-binding fragments ...

    In lead optimization, small, enthalpically advantaged fragments have been suggested to be superior, as an entropic component will be added inevitably during late-stage optimization. Determination of thermodynamic signatures of weak-binding fragments is essential to support the decision-making process, to decide which fragment to take to further optimization. High-resolution crystal structures of six fragments binding to the S1 pocket of thrombin were determined and analyzed with respect to their thermodynamic profile. The two most potent fragments exhibiting an amidine-type scaffold are not the most enthalpic binders; instead a chloro-thiophene fragment binds more enthalpically. Two chemically very similar chloro-aromatic fragments differ strongly in their potency (430 μM vs 10 mM); their binding modes are related, but the surrounding residual water network differs. The more potent one recruits a water molecule and involves Glu192 in binding, thus succeeding in firmly capping the S1 pocket. Fragments exhibiting a rather perfect solvation pattern in their binding mode also experience the highest potency.


    Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marbacher Weg 6, 35037 Marburg, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN HEAVY CHAIN
H
258Homo 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
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIRUDIN VARIANT-2
I
12Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
THROMBIN LIGHT CHAIN
L
29Homo 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
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SJR
Query on SJR

Download CCD File 
H
4-methoxy-N-(pyridin-2-yl)benzamide
C13 H12 N2 O2
YFXWAMDABVLKSA-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PO4
Query on PO4

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

Download CCD File 
H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
H
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
H
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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 %)
SJRKd:  1582000   nM  BindingDB
SJRKd:  1003000   nM  Binding MOAD
SJRKi:  2430000   nM  BindingDB
SJRKd:  1003000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.121 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.034α = 90
b = 71.246β = 100.38
c = 72.138γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Derived calculations, Other