SMTL ID : 6qei.1

CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR 5,6-Difluoro-3-(2-isopropoxy-4-piperazin-1-yl-phenyl)-1H-indole-2-carboxylic acid amide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: M.78, T.160, V.161, T.162, L.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.162, A:T.162 Water bridges: A:T.162 EDO.2: 10 residues within 4Å: Chain A: R.74, C.157, A.158, F.159, K.175, F.352, E.353, H.354 Ligands: GOL.3, DMS.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.74, A:K.175, A:K.175, A:E.353

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.74, K.175, H.354, R.368, G.369 Ligands: EDO.2, DMS.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.74, A:K.175, A:K.175, A:R.368

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 6 residues within 4Å: Chain A: R.74, K.75, M.78, F.159 Ligands: EDO.2, GOL.3 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.159

1 x HZE: 5,6-bis(fluoranyl)-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide(Non-covalent)

HZE.5: 16 residues within 4Å: Chain A: F.113, P.114, H.125, D.156, L.222, H.225, I.232, H.233, E.258, H.276, Y.277, M.278, A.308, Y.338, L.341 Ligands: MN.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.113, A:L.222, A:I.232, A:H.233, A:Y.338, A:Y.338, A:Y.338 pi-Cation interactions: A:H.125, A:H.125

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

MN.6: 7 residues within 4Å: Chain A: D.156, H.225, A.256, E.258, E.353 Ligands: HZE.5, MN.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.156, A:H.225, A:E.258, A:E.353, H2O.1 MN.7: 5 residues within 4Å: Chain A: F.113, D.145, D.156, E.353 Ligands: MN.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.145, A:D.156, A:E.353, H2O.1, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heinrich, T. et al., Discovery and Structure-Based Optimization of Next-Generation Reversible Methionine Aminopeptidase-2 (MetAP-2) Inhibitors. J.Med.Chem. (2019)

Release Date

2019-05-01

Peptides

Methionine aminopeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 2

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