SMTL ID : 4hxx.1

Pyridinylpyrimidines selectively inhibit human methionine aminopeptidase-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

3 x CO: COBALT (II) ION(Non-covalent)

CO.1: 6 residues within 4Å: Chain A: D.151, H.214, T.245, E.247, E.278 Ligands: CO.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.151, A:H.214, A:E.247, A:E.278, A:E.278 CO.2: 4 residues within 4Å: Chain A: D.140, D.151, E.278 Ligands: CO.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.140, A:D.140, A:D.151, A:E.278, H2O.1 CO.3: 2 residues within 4Å: Chain A: H.123 Ligands: 1AY.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.123, H2O.1, H2O.3, H2O.4

1 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: S.116, V.117, N.118, V.120, S.274 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.116, A:N.118, A:V.120, A:S.274, H2O.1

1 x 1AY: (1R)-N~2~-[5-chloro-2-(5-chloropyridin-2-yl)-6-methylpyrimidin-4-yl]-1-phenyl-N~1~-(4-phenylbutyl)ethane-1,2-diamine(Non-covalent)

1AY.5: 14 residues within 4Å: Chain A: E.39, Q.40, K.43, P.103, Y.106, F.109, C.114, H.123, C.212, H.214, H.221, E.247, W.264 Ligands: CO.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.39, A:Q.40, A:K.43, A:K.43, A:Y.106, A:Y.106, A:W.264 pi-Stacking: A:H.221

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 6 residues within 4Å: Chain A: K.6, L.7, R.8, H.10, R.129, Q.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.8, A:Q.132 Water bridges: A:R.129 Salt bridges: A:H.10, A:R.129 SO4.7: 2 residues within 4Å: Chain A: Q.197, W.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.197, A:W.255 Water bridges: A:R.209, A:R.209, A:W.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, P. et al., Pyridinylpyrimidines selectively inhibit human methionine aminopeptidase-1. Bioorg.Med.Chem. (2013)

Release Date

2013-04-03

Peptides

Methionine aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 1

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