SMTL ID : 5x1w.1

PKM2 in complex with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.451, A:K.452, A:S.453, A:S.456, A:S.456, A:S.456, A:G.533, A:R.535, A:G.537, A:G.539, A:F.540 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 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.451, B:K.452, B:S.453, B:S.456, B:S.456, B:G.533, B:R.535, B:G.537, B:S.538, B:G.539, B:F.540 Salt bridges: B:K.452, B:R.508 FBP.5: 17 residues within 4Å: Chain C: L.450, T.451, K.452, S.453, G.454, 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 C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:G.454, C:S.456, C:S.456, C:S.456, C:G.533, C:G.537, C:S.538, C:G.539, C:F.540 Salt bridges: C:K.452, C:R.508 FBP.6: 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 14 PLIP interactions: 14 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:S.456, D:G.533, D:G.537, D:G.539, D:F.540, D:F.540 Salt bridges: D:K.452, D:R.508

2 x 7Y0: 4-[2,3-bis(chloranyl)phenyl]carbonyl-N-[2-[[4-[2,3-bis(chloranyl)phenyl]carbonyl-1-methyl-pyrrol-2-yl]carbonylamino]ethyl]-1-methyl-pyrrole-2-carboxamide(Non-covalent)

7Y0.2: 23 residues within 4Å: Chain A: F.45, L.46, K.330, N.369, L.372, D.373, A.407, I.408, Y.409, Q.412, L.413, E.416 Chain B: F.45, L.46, K.330, N.369, L.372, D.373, I.408, Y.409, Q.412, L.413, E.416 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.45, B:F.45, B:F.45, B:L.413, A:F.45, A:F.45, A:L.413 Hydrogen bonds: B:Y.409, A:Y.409 Halogen bonds: B:E.416, A:E.416 pi-Stacking: A:F.45 7Y0.4: 24 residues within 4Å: Chain C: F.45, L.46, K.330, N.369, L.372, D.373, A.407, I.408, Y.409, Q.412, L.413, E.416 Chain D: F.45, L.46, K.330, N.369, L.372, D.373, A.407, I.408, Y.409, Q.412, L.413, E.416 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.45, C:L.413, D:L.413 Hydrogen bonds: C:Y.409, D:Y.409 pi-Stacking: C:F.45, D:F.45, D:F.45 Halogen bonds: C:E.416, 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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