SMTL ID : 9ftr.1

Drosophila golgi alpha-mannosidase II (dGMII) in complex with amide modified swainsonine-configured alkyl indolizidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

1 x 01: amide modified swainsonine-configured alkyl indolizidine

01.1: 15 residues within 4Å: Chain A: H.78, D.80, W.83, D.192, F.194, R.216, Y.257, D.329, W.403, H.459, D.460, Y.715, R.864 Ligands: EDO.11, ZN.24 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.83, A:F.194, A:W.403, A:Y.715 Hydrogen bonds: A:Y.257, A:D.329, A:T.465, A:T.465 Salt bridges: A:D.80, A:D.192, A:D.329, A:D.460

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

EDO.2: 7 residues within 4Å: Chain A: R.164, N.165, L.168, M.421, V.424, R.425, V.949 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: H.218, F.393, T.394, L.810, A.814, Y.817 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: K.51, Y.255, H.261, W.287 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: S.517, L.556, D.558, R.605, E.741, R.758 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: P.722, R.781, L.845, A.846, E.849 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: D.30, V.31, Q.32, E.35, L.36, R.39 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: R.962, T.1000, F.1004, L.1005, N.1007, V.1028 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: A.995, R.996, C.997, H.1010, D.1012, M.1014 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: K.138, K.142, M.181, N.182, V.183 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.216, S.256, Y.257, D.328 Ligands: 01.1 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: V.752, Q.754, R.765, L.767 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: T.784, H.785, I.786, D.787, S.847 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: S.41, F.42, K.43, K.809, L.810 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: E.147, F.148, V.183, P.185, Q.368 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: W.433, H.434, F.934, L.991 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: I.56, K.57, Y.58 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: R.952, Q.961, L.991, P.992, H.1031 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: D.506, F.509, Y.511 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: P.939, K.984, L.985, D.986, H.989, L.990 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: D.30, Q.230, R.318, P.386 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: Q.227, Q.228, R.229, R.318 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain A: L.953, R.962 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.24: 5 residues within 4Å: Chain A: H.78, D.80, D.192, H.459 Ligands: 01.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.78, A:D.80, A:D.192, A:H.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koemans, T. et al., Structure-guided design of C3-branched swainsonine as potent and selective human Golgi alpha-mannosidase (GMII) inhibitor. Chem.Commun.(Camb.) (2024)

Release Date

2024-10-09

Peptides

Alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase 2

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