SMTL ID : 6tti.1

PKM2 in complex with Compound 6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x NXE: ~{N}-[3-(trifluoromethyl)-1,2-oxazol-5-yl]ethanamide(Non-covalent)

NXE.1: 10 residues within 4Å: Chain A: F.43, H.46, M.47, L.370, D.371, A.405 Chain B: F.43, K.328 Ligands: DMS.3, NXE.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B pi-Stacking: A:F.43 Hydrophobic interactions: B:F.43 NXE.4: 10 residues within 4Å: Chain A: F.43, K.328 Chain B: F.43, H.46, M.47, L.370, D.371, A.405 Ligands: NXE.1, DMS.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.43, B:F.43 NXE.7: 10 residues within 4Å: Chain C: F.43, H.46, M.47, L.370, D.371, A.405 Chain D: F.43, K.328 Ligands: DMS.9, NXE.10 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.43, C:F.43 NXE.10: 10 residues within 4Å: Chain C: F.43, K.328 Chain D: F.43, H.46, M.47, L.370, D.371, A.405 Ligands: NXE.7, DMS.12 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C pi-Stacking: D:F.43 Hydrophobic interactions: C:F.43

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

FBP.2: 16 residues within 4Å: Chain A: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 16 PLIP interactions: 16 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 Water bridges: A:R.506, A:T.539 Salt bridges: A:K.450, A:R.506 FBP.5: 16 residues within 4Å: Chain B: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 16 PLIP interactions: 16 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 Water bridges: B:R.506, B:T.539 Salt bridges: B:K.450, B:R.506 FBP.8: 16 residues within 4Å: Chain C: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 18 PLIP interactions: 18 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:S.454, C:S.454, C:G.531, C:G.535, C:S.536, C:G.537, C:F.538 Water bridges: C:R.506, C:T.539, C:T.539 Salt bridges: C:K.450, C:R.506 FBP.11: 16 residues within 4Å: Chain D: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, R.533, P.534, G.535, S.536, G.537, F.538, T.539 18 PLIP interactions: 18 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:S.454, D:S.454, D:G.531, D:G.535, D:S.536, D:G.537, D:F.538 Water bridges: D:R.506, D:T.539, D:T.539 Salt bridges: D:K.450, D:R.506

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: L.370, I.406, Y.407 Ligands: NXE.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.407 DMS.6: 4 residues within 4Å: Chain B: L.370, I.406, Y.407 Ligands: NXE.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.407 DMS.9: 4 residues within 4Å: Chain C: L.370, I.406, Y.407 Ligands: NXE.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.407 DMS.12: 4 residues within 4Å: Chain D: L.370, I.406, Y.407 Ligands: NXE.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.407

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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