SMTL ID : 5x1v.1

PKM2 in complex with compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 16 residues within 4Å: Chain A: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.451, A:K.452, A:S.453, A:S.456, A:S.456, A:G.533, A:R.535, A:G.537, A:G.539, A:F.540 Water bridges: A:R.508, A:R.508 Salt bridges: A:K.452, A:R.508 FBP.3: 17 residues within 4Å: Chain B: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, T.532, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.451, B:K.452, B:S.453, B:G.454, B:S.456, B:S.456, B:G.533, B:G.537, B:S.538, B:G.539, B:F.540, B:T.541 Water bridges: B:W.501, B:D.504, B:T.541 Salt bridges: B:K.452, B:R.508 FBP.5: 17 residues within 4Å: Chain C: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, T.532, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:S.456, C:S.456, C:G.533, C:G.537, C:S.538, C:G.539, C:F.540 Water bridges: C:R.508, C:R.508, C:T.541 Salt bridges: C:K.452, C:R.508 FBP.7: 16 residues within 4Å: Chain D: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:T.451, D:T.451, D:K.452, D:S.453, D:S.456, D:S.456, D:G.533, D:R.535, D:G.537, D:G.539, D:F.540 Water bridges: D:R.455, D:R.508, D:R.508 Salt bridges: D:K.452, D:R.508

4 x 7XX: 4-[2,3-bis(chloranyl)phenyl]carbonyl-1-methyl-pyrrole-2-carboxamide(Non-covalent)

7XX.2: 14 residues within 4Å: Chain A: F.45, L.372, D.373, A.407, I.408, Y.409, Q.412, L.413, E.416 Chain B: F.45, L.46, M.49, K.330 Ligands: 7XX.4 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.413 Hydrogen bonds: A:N.369, A:Y.409 pi-Stacking: A:F.45, B:F.45 Halogen bonds: A:E.416 Water bridges: B:K.330, B:K.330, B:D.373, B:D.373 7XX.4: 15 residues within 4Å: Chain A: F.45, L.46, M.49, K.330 Chain B: F.45, H.48, L.372, D.373, A.407, I.408, Y.409, Q.412, L.413, E.416 Ligands: 7XX.2 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Water bridges: A:K.330, A:N.369, A:N.369, A:D.373, A:D.373, B:N.369, B:L.372 pi-Stacking: A:F.45, B:F.45 Hydrophobic interactions: B:L.413 Hydrogen bonds: B:Y.409 Halogen bonds: B:E.416 7XX.6: 15 residues within 4Å: Chain C: F.45, H.48, L.372, D.373, A.407, I.408, Y.409, Q.412, L.413, E.416 Chain D: F.45, L.46, M.49, K.330 Ligands: 7XX.8 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.413, D:F.45 Hydrogen bonds: C:Y.409 Water bridges: C:L.372, D:K.330, D:N.369, D:D.373 pi-Stacking: C:F.45 Halogen bonds: C:E.416 7XX.8: 15 residues within 4Å: Chain C: F.45, L.46, M.49, K.330 Chain D: F.45, H.48, L.372, D.373, A.407, I.408, Y.409, Q.412, L.413, E.416 Ligands: 7XX.6 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.413, C:L.46 Hydrogen bonds: D:Y.409, C:K.330 pi-Stacking: D:F.45, C:F.45 Halogen bonds: D:E.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsui, Y. et al., Discovery and structure-guided fragment-linking of 4-(2,3-dichlorobenzoyl)-1-methyl-pyrrole-2-carboxamide as a pyruvate kinase M2 activator. Bioorg. Med. Chem. (2017)

Release Date

2017-05-31

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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