3NN7

Crystal structure of Thermolysin in complex with 2-bromoacetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Experimental and computational active site mapping as a starting point to fragment-based lead discovery.

Behnen, J.Koster, H.Neudert, G.Craan, T.Heine, A.Klebe, G.

(2012) Chemmedchem 7: 248-261

  • DOI: 10.1002/cmdc.201100490
  • Primary Citation of Related Structures:  3MS3, 3MSA, 3MSF, 3MSN, 3N21, 3N4A, 3N9W, 3NX8, 3PCZ, 3PRS, 3PVK, 3PWW

  • PubMed Abstract: 
  • Small highly soluble probe molecules such as aniline, urea, N-methylurea, 2-bromoacetate, 1,2-propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of bi ...

    Small highly soluble probe molecules such as aniline, urea, N-methylurea, 2-bromoacetate, 1,2-propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of binding with respect to hydrophobic and hydrophilic properties. The selected probe molecules were first tested at the zinc protease thermolysin. They were then applied to a wider range of proteins such as protein kinase A, D-xylose isomerase, 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, endothiapepsin, and secreted aspartic protease 2. The crystal structures obtained clearly show that the probe molecules populate the protein binding pockets in an ordered fashion. The thus characterized, experimentally observed hot spots of binding were subjected to computational active site mapping using HotspotsX. This approach uses knowledge-based pair potentials to detect favorable binding positions for various atom types. Good agreement between the in silico hot spot predictions and the experimentally observed positions of the polar hydrogen bond forming functional groups and hydrophobic portions was obtained. Finally, we compared the observed poses of the small-molecule probes with those of much larger structurally related ligands. They coincide remarkably well with the larger ligands, considering their spatial orientation and the experienced interaction patterns. This observation confirms the fundamental hypothesis of fragment-based lead discovery: that binding poses, even of very small molecular probes, do not significantly deviate or move once a ligand is grown further into the binding site. This underscores the fact that these probes populate given hot spots and can be regarded as relevant seeds for further design.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Bacillus thermoproteolyticusGene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BXA
Query on BXA

Download SDF File 
Download CCD File 
A
bromoacetic acid
C2 H3 Br O2
KDPAWGWELVVRCH-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.173 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.947α = 90.00
b = 92.947β = 90.00
c = 129.951γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXL-97refinement
CrystalCleardata collection
CNSphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-01-18
    Type: Database references
  • Version 1.3: 2012-02-15
    Type: Database references