SMTL ID : 6qef.1

CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR (S)-3-Hydroxy-2-oxo-1-phenyl-pyrrolidine-3-carboxylic acid 3-chloro-5-fluoro-benzylamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: M.78, T.160, V.161, T.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.162, A:T.162 Water bridges: A:T.162, A:D.168 EDO.2: 4 residues within 4Å: Chain A: E.104, G.106, N.303, L.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.106, A:N.303 EDO.3: 8 residues within 4Å: Chain A: R.74, C.157, A.158, F.159, F.352, E.353, H.354 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.74, A:E.353 EDO.4: 3 residues within 4Å: Chain A: E.92, D.96, R.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.316 EDO.5: 5 residues within 4Å: Chain A: P.9, P.10, Y.76, C.97, K.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.100 Water bridges: A:Y.76, A:C.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.74, H.354, R.368 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.74, A:R.74, A:R.368, A:R.368

1 x HZW: (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-phenyl-pyrrolidine-3-carboxamide(Non-covalent)

HZW.7: 20 residues within 4Å: Chain A: F.113, A.124, H.125, D.145, D.156, L.222, N.223, H.225, I.232, H.233, E.258, F.260, H.276, M.278, A.308, Y.338, Q.351, E.353 Ligands: MN.8, MN.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.124, A:L.222, A:I.232, A:A.308, A:Y.338 Hydrogen bonds: A:H.125, A:Q.351 pi-Stacking: A:H.233 pi-Cation interactions: A:H.125

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

MN.8: 7 residues within 4Å: Chain A: D.156, H.225, A.256, E.258, E.353 Ligands: HZW.7, MN.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.156, A:H.225, A:E.258, A:E.353 MN.9: 6 residues within 4Å: Chain A: D.145, D.156, Q.351, E.353 Ligands: HZW.7, MN.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.145, A:D.145, A:D.156, A:E.353

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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