SMTL ID : 7a12.1

CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GW557358X (COMPOUND 9)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: H.124, L.221, N.222, H.224, E.257, F.259 Ligands: QVK.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.222, A:N.222, A:E.257 Water bridges: A:H.124, A:N.222, A:Q.350 Salt bridges: A:H.124 PO4.2: 5 residues within 4Å: Chain A: T.161, F.162, N.163, P.164, D.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.161, A:T.161, A:F.162 PO4.3: 6 residues within 4Å: Chain A: C.273, Y.276, R.310, L.322, L.325, K.326 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.273, A:R.310 PO4.4: 4 residues within 4Å: Chain A: Y.229, F.303, G.304, T.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.305, A:L.306 PO4.5: 7 residues within 4Å: Chain A: M.77, F.158, T.159, K.174, F.351, D.370, Y.371 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.159, A:T.159, A:D.370 Salt bridges: A:K.174 PO4.6: 2 residues within 4Å: Chain A: H.284, N.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.300 Salt bridges: A:H.284 PO4.7: 3 residues within 4Å: Chain A: L.289, N.327, L.331 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.327 PO4.8: 4 residues within 4Å: Chain A: H.294, N.297, V.298, E.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.301 Salt bridges: A:H.294 PO4.9: 9 residues within 4Å: Chain A: F.112, P.113, H.124, I.231, H.275, M.277, A.307, Y.337 Ligands: QVK.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.124, A:H.124 Salt bridges: A:H.124

1 x QVK: 5-chloranyl-3-phenyl-1~{H}-indole-2-carboxamide(Non-covalent)

QVK.10: 15 residues within 4Å: Chain A: F.112, H.124, D.155, H.224, I.231, H.232, E.257, H.275, Y.276, M.277, A.307, Y.337 Ligands: PO4.1, PO4.9, MN.12 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.112, A:H.232, A:A.307, A:Y.337 Hydrogen bonds: A:H.224 Water bridges: A:H.124, A:D.144, A:D.155 pi-Stacking: A:Y.337 pi-Cation interactions: A:H.124, A:H.124

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

MN.11: 4 residues within 4Å: Chain A: D.144, D.155, E.352 Ligands: MN.12 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.144, A:D.155, A:E.352, H2O.1, H2O.7 MN.12: 7 residues within 4Å: Chain A: D.155, H.224, A.255, E.257, E.352 Ligands: QVK.10, MN.11 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.155, A:E.257, A:E.352, H2O.1, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirst, D.J. et al., Structure-based optimisation of orally active & reversible MetAP-2 inhibitors maintaining a tight 'molecular budget'. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-09-23

Peptides

Methionine aminopeptidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase 2

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