SMTL ID : 6ttf.1

PKM2 in complex with Compound 5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x LZ2: 5-hydroxynaphthalene-1-sulfonamide

LZ2.1: 11 residues within 4Å: Chain A: F.43, L.370, D.371, I.406, Y.407, Q.410, L.411, E.414 Chain B: F.43, L.44, M.47 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.411, B:L.44 Hydrogen bonds: A:Y.407 pi-Stacking: B:F.43 LZ2.3: 11 residues within 4Å: Chain A: F.43, L.44, M.47 Chain B: F.43, L.370, D.371, I.406, Y.407, Q.410, L.411, E.414 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.44, B:L.411 pi-Stacking: A:F.43 Hydrogen bonds: B:Y.407 LZ2.5: 11 residues within 4Å: Chain C: F.43, L.370, D.371, I.406, Y.407, Q.410, L.411, E.414 Chain D: F.43, L.44, M.47 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.44, C:L.411 pi-Stacking: D:F.43 Hydrogen bonds: C:Y.407 LZ2.7: 11 residues within 4Å: Chain C: F.43, L.44, M.47 Chain D: F.43, L.370, D.371, I.406, Y.407, Q.410, L.411, E.414 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.411, C:L.44 Hydrogen bonds: D:Y.407 pi-Stacking: C:F.43

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.2: 17 residues within 4Å: Chain A: L.448, T.449, K.450, S.451, G.452, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.449, A:K.450, A:S.451, A:G.452, A:R.453, A:S.454, A:S.454, A:G.531, A:G.535, A:S.536, A:G.537, A:F.538 Salt bridges: A:R.506 FBP.4: 17 residues within 4Å: Chain B: L.448, T.449, K.450, S.451, G.452, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.449, B:K.450, B:S.451, B:G.452, B:R.453, B:S.454, B:S.454, B:G.531, B:G.535, B:S.536, B:G.537, B:F.538 Salt bridges: B:R.506 FBP.6: 17 residues within 4Å: Chain C: L.448, T.449, K.450, S.451, G.452, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.449, C:K.450, C:S.451, C:G.452, C:R.453, C:S.454, C:G.531, C:G.535, C:G.537, C:F.538 Salt bridges: C:R.506 FBP.8: 17 residues within 4Å: Chain D: L.448, T.449, K.450, S.451, G.452, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:T.449, D:K.450, D:S.451, D:G.452, D:R.453, D:S.454, D:G.531, D:G.535, D:G.537, D:F.538 Salt bridges: D:R.506

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saur, M. et al., Fragment-based drug discovery using cryo-EM. Drug Discov Today (2020)

Release Date

2020-01-15

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM

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