5LIF

Thermolysin in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin.

Cramer, J.Krimmer, S.G.Fridh, V.Wulsdorf, T.Karlsson, R.Heine, A.Klebe, G.

(2017) ACS Chem. Biol. 12: 225-233

  • DOI: 10.1021/acschembio.6b00979
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kinetic parameters of protein-ligand interactions are progressively acknowledged as valuable information for rational drug discovery. However, a targeted optimization of binding kinetics is not easy to achieve, and further systematic studies are nece ...

    Kinetic parameters of protein-ligand interactions are progressively acknowledged as valuable information for rational drug discovery. However, a targeted optimization of binding kinetics is not easy to achieve, and further systematic studies are necessary to increase the understanding about molecular mechanisms involved. We determined association and dissociation rate constants for 17 inhibitors of the metalloprotease thermolysin by surface plasmon resonance spectroscopy and correlated kinetic data with high-resolution crystal structures in complex with the protein. From the structure-kinetics relationship, we conclude that the strength of interaction with Asn112 correlates with the rate-limiting step of dissociation. This residue is located at the beginning of a β-strand motif that lines the binding cleft and is commonly believed to align a substrate for catalysis. A reduced mobility of the Asn112 side chain owing to an enhanced engagement in charge-assisted hydrogen bonds prevents the conformational adjustment associated with ligand release and transformation of the enzyme to its open state. This hypothesis is supported by kinetic data of ZFPLA, a known pseudopeptidic inhibitor of thermolysin, which blocks the conformational transition of Asn112. Interference with this retrograde induced-fit mechanism results in variation of the residence time of thermolysin inhibitors by a factor of 74 000. The high conservation of this structural motif within the M4 and M13 metalloprotease families underpins the importance of this feature and has significant implications for drug discovery.


    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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Download CCD File 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
E
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
6XO
Query on 6XO

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Download CCD File 
E
(2~{S})-3-cyclohexyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]propanoic acid
C24 H38 N3 O7 P
XUMUUEQXPBWJGZ-SFTDATJTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.113 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.801α = 90.00
b = 91.801β = 90.00
c = 130.010γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany268145-DrugProfilBind

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Database references