SMTL ID : 3ddg.1

GOLGI MANNOSIDASE II complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)-2-hydroxy-1 phenylethyl]amino}methyl) methylpyrrolidin-2-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 1 residues within 4Å: Chain A: N.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.194

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: R.893, S.924 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.924 Water bridges: A:R.893 Salt bridges: A:R.893

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.90, D.92, D.204, H.471 Ligands: GB7.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.90, A:D.92, A:D.204, A:H.471

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 5 residues within 4Å: Chain A: K.63, Q.64, Y.267, H.273, P.279 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.63, A:Y.267, A:Y.267, A:Y.267 Water bridges: A:Q.64

1 x GB7: (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-1-methylpyrrolidin-2-one(Non-covalent)

GB7.5: 15 residues within 4Å: Chain A: H.90, D.92, W.95, D.204, F.206, R.228, Y.269, D.340, D.341, H.471, D.472, Y.727, R.876, G.877 Ligands: ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.269, A:Y.269, A:D.340, A:Y.727 Water bridges: A:R.228, A:S.268 pi-Stacking: A:W.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fiaux, H. et al., Functionalized pyrrolidine inhibitors of human type II alpha-mannosidases as anti-cancer agents: optimizing the fit to the active site. Bioorg.Med.Chem. (2008)

Release Date

2008-07-01

Peptides

alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

alpha-mannosidase 2

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