SMTL ID : 6ttq.1

PKM2 in complex with Compound 10

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x NXH: 1-propan-2-yl-3-pyridin-4-yl-urea(Non-covalent)

NXH.1: 9 residues within 4Å: Chain A: F.43, A.405, I.406, Y.407, Q.410, L.411 Chain B: F.43, K.328 Ligands: NXH.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.43, A:L.411 Hydrogen bonds: A:Y.407 NXH.3: 9 residues within 4Å: Chain A: F.43, K.328 Chain B: F.43, A.405, I.406, Y.407, Q.410, L.411 Ligands: NXH.1 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.43, B:L.411 Hydrogen bonds: B:Y.407 Water bridges: B:L.370 NXH.5: 9 residues within 4Å: Chain C: F.43, A.405, I.406, Y.407, Q.410, L.411 Chain D: F.43, K.328 Ligands: NXH.7 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.43, C:L.411 Hydrogen bonds: C:Y.407 Water bridges: C:L.370, D:D.371 NXH.7: 9 residues within 4Å: Chain C: F.43, K.328 Chain D: F.43, A.405, I.406, Y.407, Q.410, L.411 Ligands: NXH.5 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.43, D:L.411 Hydrogen bonds: D:Y.407 Water bridges: C:D.371

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 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.449, A:K.450, A:S.451, A:R.453, A:S.454, A:S.454, A:S.454, A:G.531, A:G.535, A:S.536, A:G.537, A:F.538, A:F.538 Salt bridges: A:K.450, A:R.506 FBP.4: 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 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.449, B:K.450, B:S.451, B:R.453, B:S.454, B:S.454, B:S.454, B:G.531, B:G.535, B:S.536, B:G.537, B:F.538, B:F.538 Salt bridges: B:K.450, B:R.506 FBP.6: 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 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.449, C:K.450, C:S.451, C:R.453, C:S.454, C:S.454, C:G.531, C:G.535, C:S.536, C:G.537, C:F.538, C:F.538 Salt bridges: C:K.450, C:R.506 FBP.8: 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 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.449, D:K.450, D:S.451, D:R.453, D:S.454, D:S.454, D:G.531, D:G.535, D:S.536, D:G.537, D:F.538, D:F.538 Salt bridges: D:K.450, 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

Related Entries With Identical Sequence