SMTL ID : 7a15.1

CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2224863A (COMPOUND 42)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: T.161, F.162, N.163, P.164, D.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.161, A:T.161, A:F.162 Water bridges: A:D.167 PO4.2: 5 residues within 4Å: Chain A: C.273, Y.276, R.310, L.325, K.326 1 PLIP interactions: 1 interactions with chain A Water bridges: A:C.273 PO4.3: 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:D.370 Water bridges: A:D.370 Salt bridges: A:K.174 PO4.4: 2 residues within 4Å: Chain A: H.284, N.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.300 Water bridges: A:V.285 Salt bridges: A:H.284 PO4.5: 3 residues within 4Å: Chain A: L.289, N.327, L.331 No protein-ligand interaction detected (PLIP) PO4.6: 5 residues within 4Å: Chain A: E.27, C.28, E.29, T.43, C.361 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.27 PO4.7: 4 residues within 4Å: Chain A: S.55, I.58, W.59, G.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.55, A:S.55

1 x QV5: 5-chloranyl-6-fluoranyl-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide(Non-covalent)

QV5.8: 16 residues within 4Å: Chain A: F.112, P.113, H.124, D.155, L.221, H.224, I.231, H.232, E.257, H.275, Y.276, M.277, A.307, Y.337, L.340 Ligands: MN.10 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.112, A:L.221, A:I.231, A:H.232, A:Y.337 Water bridges: A:H.124, A:D.144, A:D.155, A:N.222, A:R.230, A:H.232 pi-Cation interactions: A:H.124, A:H.124

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

MN.9: 5 residues within 4Å: Chain A: F.112, D.144, D.155, E.352 Ligands: MN.10 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.9 MN.10: 7 residues within 4Å: Chain A: D.155, H.224, A.255, E.257, E.352 Ligands: QV5.8, MN.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:H.224, A:E.257, A:E.352, H2O.1

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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