SMTL ID : 4flk.1

Human MetAP1 with bengamide analog Y10, in Mn form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: D.152, H.215, T.246, E.248, E.279 Ligands: MN.2, Y10.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.152, A:H.215, A:E.248, A:E.279 MN.2: 5 residues within 4Å: Chain A: D.141, D.152, E.279 Ligands: MN.1, Y10.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.141, A:D.141, A:D.152, A:E.279

1 x Y10: (E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide(Non-covalent)

Y10.3: 19 residues within 4Å: Chain A: P.104, Y.107, C.115, H.124, D.141, T.143, D.152, Y.212, C.213, H.215, F.221, H.222, E.248, M.250, W.265, Q.277, E.279 Ligands: MN.1, MN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.221, A:F.221, A:H.222, A:W.265 Hydrogen bonds: A:C.213 Water bridges: A:T.143, A:Q.277, A:Q.277 pi-Stacking: A:H.222

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: V.118, N.119, V.121, S.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.117, A:S.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, W. et al., Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases. J.Med.Chem. (2012)

Release Date

2012-09-19

Peptides

Methionine aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 1

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