SMTL ID : 2g6p.1

Crystal structure of truncated (delta 1-89) human methionine aminopeptidase Type 1 in complex with Pyridyl pyrimidine derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.151, A:H.214, A:E.247, A:E.278, H2O.5 CO.2: 4 residues within 4Å: Chain A: D.140, D.151, E.278 Ligands: CO.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.140, A:D.151, A:E.278, H2O.1, H2O.5 CO.3: 2 residues within 4Å: Chain A: H.123 Ligands: HM2.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.123, H2O.1, H2O.1, H2O.1

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.2

1 x HM2: 5-CHLORO-6-METHYL-N-(2-PHENYLETHYL)-2-PYRIDIN-2-YLPYRIMIDIN-4-AMINE(Non-covalent)

HM2.5: 9 residues within 4Å: Chain A: Y.106, F.109, C.114, H.123, Y.211, H.221, W.264 Ligands: CO.3, EPE.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.106, A:F.109, A:F.109, A:Y.211, A:W.264, A:W.264 Hydrogen bonds: A:Y.106 pi-Stacking: A:H.123, A:H.221

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 4 residues within 4Å: Chain A: Y.107, G.263, W.264 Ligands: HM2.5 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.264

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: T.83, T.115, S.116, V.117, V.120, I.125, P.126, D.127, R.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.83, A:V.117, A:D.127, A:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, X. et al., Identification of Pyridinylpyrimidines as Inhibitors of Human Methionine Aminopeptidases. Angew.Chem.Int.Ed.Engl. (2006)

Release Date

2006-06-20

Peptides

Methionine aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 1

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