1QZY

Human Methionine Aminopeptidase in complex with bengamide inhibitor LAF153 and cobalt


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Proteomics-based target identification: bengamides as a new class of methionine aminopeptidase inhibitors.

Towbin, H.Bair, K.W.DeCaprio, J.A.Eck, M.J.Kim, S.Kinder, F.R.Morollo, A.Mueller, D.R.Schindler, P.Song, H.K.van Oostrum, J.Versace, R.W.Voshol, H.Wood, J.Zabludoff, S.Phillips, P.E.

(2003) J.Biol.Chem. 278: 52964-52971

  • DOI: 10.1074/jbc.M309039200

  • PubMed Abstract: 
  • LAF389 is a synthetic analogue of bengamides, a class of marine natural products that produce inhibitory effects on tumor growth in vitro and in vivo. A proteomics-based approach has been used to identify signaling pathways affected by bengamides. LA ...

    LAF389 is a synthetic analogue of bengamides, a class of marine natural products that produce inhibitory effects on tumor growth in vitro and in vivo. A proteomics-based approach has been used to identify signaling pathways affected by bengamides. LAF389 treatment of cells resulted in altered mobility of a subset of proteins on two-dimensional gel electrophoresis. Detailed analysis of one of the proteins, 14-3-3gamma, showed that bengamide treatment resulted in retention of the amino-terminal methionine, suggesting that bengamides directly or indirectly inhibited methionine aminopeptidases (MetAps). Both known MetAps are inhibited by LAF389. Short interfering RNA suppression of MetAp2 also altered amino-terminal processing of 14-3-3gamma. A high resolution structure of human MetAp2 co-crystallized with a bengamide shows that the compound binds in a manner that mimics peptide substrates. Additionally, the structure reveals that three key hydroxyl groups on the inhibitor coordinate the di-cobalt center in the enzyme active site.


    Organizational Affiliation

    Novartis Pharma AG, CH-4036 Basle, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase 2
A
478Homo sapiensMutation(s): 0 
Gene Names: METAP2 (MNPEP, P67EIF2)
EC: 3.4.11.18
Find proteins for P50579 (Homo sapiens)
Go to Gene View: METAP2
Go to UniProtKB:  P50579
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDE
Query on TDE

Download SDF File 
Download CCD File 
A
(E)-(2R,3R,4S,5R)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-NON-6-ENOIC ACID ((3S,6R)-6-HYDROXY-2-OXO-AZEPAN-3-YL)-AMIDE
C18 H32 N2 O7
FVBBTOIQETYGOA-SDNORSGYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
TBU
Query on TBU

Download SDF File 
Download CCD File 
A
TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TDEIC50: ~800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.610α = 90.00
b = 99.040β = 90.00
c = 101.383γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance