SMTL ID : 8oxg.1

Crystal structure of human methionine aminopeptidase-2 complexed with (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methyl-2-buten-1-yl)-2-oxiranyl]-1-oxaspiro[2.5]oct-6-yl N-(trans-4-aminocyclohexyl)carbamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x W5N: [(1~{R},2~{S},3~{S},4~{R})-2-methoxy-4-methyl-3-[(2~{R},3~{S})-2-methyl-3-(3-methylbut-2-enyl)oxiran-2-yl]-4-oxidanyl-cyclohexyl] ~{N}-(4-azanylcyclohexyl)carbamate(Covalent)

W5N.1: 22 residues within 4Å: Chain A: F.125, P.126, A.136, H.137, N.233, L.234, N.235, G.236, H.237, I.244, H.245, T.249, E.270, F.272, V.280, H.288, M.290, A.320, Y.350, L.353 Ligands: MN.2, MN.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.125, A:L.234, A:I.244, A:A.320, A:Y.350, A:Y.350, A:L.353, A:L.353 Hydrogen bonds: A:N.235, A:N.235, A:H.237 Water bridges: A:D.168, A:H.245, A:E.270, A:D.282, A:D.282 W5N.4: 24 residues within 4Å: Chain A: C.27, D.28 Chain B: F.125, P.126, A.136, H.137, N.233, L.234, N.235, G.236, H.237, I.244, H.245, T.249, E.270, F.272, V.280, H.288, M.290, A.320, Y.350, L.353 Ligands: MN.5, MN.6 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.125, B:L.234, B:I.244, B:H.245, B:A.320, B:Y.350, B:Y.350, B:L.353 Hydrogen bonds: B:N.235, B:N.235, B:H.237, A:C.27 Water bridges: B:H.137, B:D.168, B:H.245, B:E.270

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

MN.2: 9 residues within 4Å: Chain A: F.125, D.157, D.168, A.170, E.270, Q.363, E.365 Ligands: W5N.1, MN.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.157, A:D.168, A:E.365, H2O.3, H2O.9 MN.3: 7 residues within 4Å: Chain A: D.168, H.237, A.268, E.270, E.365 Ligands: W5N.1, MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.168, A:H.237, A:E.270, A:E.365, H2O.3 MN.5: 9 residues within 4Å: Chain B: F.125, D.157, D.168, A.170, E.270, Q.363, E.365 Ligands: W5N.4, MN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.157, B:D.168, B:E.365, H2O.13, H2O.19 MN.6: 7 residues within 4Å: Chain B: D.168, H.237, A.268, E.270, E.365 Ligands: W5N.4, MN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.168, B:H.237, B:E.270, B:E.365, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cornelius, P. et al., Pharmacological Characterization of SDX-7320/Evexomostat: A Novel Methionine Aminopeptidase Type 2 Inhibitor with Anti-tumor and Anti-metastatic Activity. Mol.Cancer Ther. (2024)

Release Date

2024-04-10

Peptides

Methionine aminopeptidase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methionine aminopeptidase 2