2F1B

GOLGI ALPHA-MANNOSIDASE II COMPLEX WITH (2R,3R,4S,5R)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-5-methylpyrrolidine-3,4-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.

Englebienne, P.Fiaux, H.Kuntz, D.A.Corbeil, C.R.Gerber-Lemaire, S.Rose, D.R.Moitessier, N.

(2007) Proteins 69: 160-176

  • DOI: 10.1002/prot.21479
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexe ...

    Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.


    Organizational Affiliation

    Department of Chemistry, McGill University, Montréal, Québec H3A 2K6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alpha-mannosidase II
A
1045Drosophila melanogasterMutation(s): 0 
Gene Names: alpha-Man-IIa (GmII)
EC: 3.2.1.114
Find proteins for Q24451 (Drosophila melanogaster)
Go to UniProtKB:  Q24451
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
GB3
Query on GB3

Download SDF File 
Download CCD File 
A
(2R,3R,4S,5R)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)-5-METHYLPYRROLIDINE-3,4-DIOL
C14 H22 N2 O3
KHLOMLBNZUMIHX-QKGWFMCXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GB3IC50: 1000000 nM BINDINGMOAD
GB3IC50: 1000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.433α = 90.00
b = 110.578β = 90.00
c = 139.890γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance