SMTL ID : 5wg8.1

Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled in the density

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.105, N.137, H.186, H.261 Ligands: MN.2, LB1.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.105, A:H.186, A:H.261 MN.2: 5 residues within 4Å: Chain A: D.76, H.78, D.105 Ligands: MN.1, LB1.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.76, A:H.78, A:D.105

1 x LB1: (1S,2R,3S,4R)-3-(4-methylpiperazine-1-carbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid(Non-covalent)

LB1.3: 15 residues within 4Å: Chain A: D.76, H.78, D.105, R.109, N.137, H.138, H.186, R.234, H.261, E.262, V.263, F.280, Y.285 Ligands: MN.1, MN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.263, A:F.280, A:Y.285 Water bridges: A:N.137

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 6 residues within 4Å: Chain A: N.142, M.143, P.210, D.211, W.220, V.236 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.236 Hydrogen bonds: A:N.142 Water bridges: A:D.211, A:D.211

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 7 residues within 4Å: Chain A: K.26, Q.30, K.33, L.85, F.88, E.89, L.93 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.33, A:F.88, A:E.89, A:L.93 Water bridges: A:Q.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

D'Arcy, B.M. et al., The Antitumor Drug LB-100 Is a Catalytic Inhibitor of Protein Phosphatase 2A (PPP2CA) and 5 (PPP5C) Coordinating with the Active-Site Catalytic Metals in PPP5C. Mol. Cancer Ther. (2019)

Release Date

2018-07-18

Peptides

Serine/threonine-protein phosphatase 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serine/threonine-protein phosphatase 5

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