SMTL ID : 6qed.1

CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX; WITH AN INHIBITOR (S)-3-Hydroxy-2-oxo-1-(2-oxo-1,2,3,4-tetrahydro-quinolin-6-yl)-pyrrolidine-3-carboxylic acid 3-chloro-5-fluoro-benzylamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 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: 3 residues within 4Å: Chain A: Y.277, L.323, K.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.323 EDO.3: 8 residues within 4Å: Chain A: R.74, C.157, A.158, F.159, F.352, E.353, H.354 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.74, A:E.353

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

DMS.4: 2 residues within 4Å: Chain A: P.337, Y.338 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.336 pi-Cation interactions: A:Y.338

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: R.74, H.354, R.368 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.74, A:R.74, A:R.368

1 x HZK: (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)pyrrolidine-3-carboxamide(Non-covalent)

HZK.6: 22 residues within 4Å: Chain A: F.113, A.124, H.125, D.145, D.156, N.221, L.222, N.223, H.225, I.232, H.233, E.258, F.260, H.276, M.278, A.308, Y.338, L.341, Q.351, E.353 Ligands: MN.7, MN.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.124, A:L.222, A:I.232, A:A.308, A:Y.338, A:L.341 Hydrogen bonds: A:H.125, A:N.223, A:N.223, A:Q.351 pi-Stacking: A:H.233 pi-Cation interactions: A:H.125

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

MN.7: 7 residues within 4Å: Chain A: D.156, H.225, A.256, E.258, E.353 Ligands: HZK.6, MN.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.156, A:H.225, A:E.258, A:E.353 MN.8: 7 residues within 4Å: Chain A: F.113, D.145, D.156, Q.351, E.353 Ligands: HZK.6, MN.7 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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