5N2X

Thermolysin in complex with inhibitor JC272


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.209 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.111 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors.

Cramer, J.Krimmer, S.G.Heine, A.Klebe, G.

(2017) J. Med. Chem. 60: 5791-5799

  • DOI: 10.1021/acs.jmedchem.7b00490
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In lead optimization, open, solvent-exposed protein pockets are often disregarded as prospective binding sites. Because of bulk-solvent proximity, researchers are instead enticed to attach charged polar groups at inhibitor scaffolds to improve solubi ...

    In lead optimization, open, solvent-exposed protein pockets are often disregarded as prospective binding sites. Because of bulk-solvent proximity, researchers are instead enticed to attach charged polar groups at inhibitor scaffolds to improve solubility and pharmacokinetic properties. It is rarely considered that solvent effects from water reorganization in the first hydration shell of protein-ligand complexes can have a significant impact on binding. We investigate the thermodynamic fingerprint of thermolysin inhibitors featuring terminal charged ammonium groups that are gradually pulled from a distal, solvent-exposed position into the flat, bowl-shaped S2' pocket. Even for the most remote attachment, costs for partial desolvation of the polar group next to the protein-solvent interface are difficult to compensate by interactions with the protein or surrounding water molecules. Through direct comparison with hydrophobic analogues, a significant 180-fold affinity loss was recorded, which questions popular strategies to attach polar ligand-solubilizing groups at the exposed terminus of substituents accommodated in flat open pockets.


    Organizational Affiliation

    Institute of Pharmaceutical Chemistry, University of Marburg , Marbacher Weg 6, 35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
E
316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
8KN
Query on 8KN

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E
(2~{S})-5-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]pentanoic acid
C20 H33 N4 O7 P
WVIBWHYQVPNZPE-IRXDYDNUSA-N
 Ligand Interaction
DMS
Query on DMS

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E
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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E
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.209 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.111 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.751α = 90.00
b = 92.751β = 90.00
c = 130.348γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-07-26
    Type: Database references