SMTL ID : 4ikt.1

Crystal structure of truncated (delta 1-89) human methionine aminopeptidase Type 1 in complex with N1-(5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl)-N2-(5-(trifluoromethyl)pyridin-2-yl)ethane-1,2-diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x TFV: N-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-N'-[5-(trifluoromethyl)pyridin-2-yl]ethane-1,2-diamine(Non-covalent)

TFV.1: 12 residues within 4Å: Chain A: Y.131, F.134, C.139, H.148, C.237, H.239, H.246, T.247, A.248, N.250, W.289 Ligands: CO.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.131, A:F.134, A:F.134, A:H.246, A:W.289 Hydrogen bonds: A:E.64, A:E.64, A:Y.131 pi-Stacking: A:H.246

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

CO.2: 6 residues within 4Å: Chain A: D.176, H.239, T.270, E.272, E.303 Ligands: CO.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.176, A:H.239, A:E.272, A:E.303, H2O.4 CO.3: 5 residues within 4Å: Chain A: D.165, T.167, D.176, E.303 Ligands: CO.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.165, A:D.176, A:E.303, H2O.1, H2O.4 CO.4: 2 residues within 4Å: Chain A: H.148 Ligands: TFV.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.148, H2O.3, H2O.3, H2O.4

1 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: S.141, V.142, N.143, V.145, S.299 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.141, A:N.143, A:V.145, A:S.299, H2O.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: L.32, T.108, T.140, S.141, V.142, V.145, I.150, P.151, D.152, R.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.108, A:V.142 Water bridges: A:R.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kishor, C. et al., Identification, Biochemical and Structural Evaluation of Species-Specific Inhibitors against Type I Methionine Aminopeptidases. J.Med.Chem. (2013)

Release Date

2013-12-11

Peptides

Methionine aminopeptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 1

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