SMTL ID : 8g2e.1

PKM2 bound to compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

4 x YII: 3-[(3-aminophenyl)methyl]-5-methyl-7-[methyl(oxidanyl)-$l^{3}-sulfanyl]pyridazino[4,5-b]indol-4-one(Non-covalent)

YII.1: 19 residues within 4Å: Chain A: F.45, L.46, M.49, L.372, I.408, Y.409, Q.412, L.413 Chain B: F.45, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 Ligands: EDO.3, YII.18, EDO.20 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.46, A:Y.409, B:F.45, B:F.45, B:F.45, B:L.413, B:L.413 Hydrogen bonds: A:Y.409, B:L.372 pi-Stacking: A:F.45, A:F.45, A:F.45, B:F.45 YII.18: 19 residues within 4Å: Chain A: F.45, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 Chain B: F.45, L.46, M.49, L.372, I.408, Y.409, Q.412, L.413 Ligands: YII.1, EDO.3, EDO.20 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.45, A:F.45, A:F.45, A:L.413, A:L.413, B:L.46, B:Y.409 Hydrogen bonds: A:L.372, B:Y.409 pi-Stacking: A:F.45, B:F.45, B:F.45, B:F.45 YII.35: 19 residues within 4Å: Chain C: F.45, L.46, M.49, L.372, I.408, Y.409, Q.412, L.413 Chain D: F.45, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 Ligands: EDO.37, YII.52, EDO.54 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:L.46, C:Y.409, D:F.45, D:F.45, D:F.45, D:L.413, D:L.413 Hydrogen bonds: C:Y.409, D:L.372 pi-Stacking: C:F.45, C:F.45, C:F.45, D:F.45 YII.52: 19 residues within 4Å: Chain C: F.45, N.337, L.372, D.373, Y.409, Q.412, L.413, E.416 Chain D: F.45, L.46, M.49, L.372, I.408, Y.409, Q.412, L.413 Ligands: YII.35, EDO.37, EDO.54 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:F.45, C:F.45, C:F.45, C:L.413, C:L.413, D:L.46, D:Y.409 Hydrogen bonds: C:L.372, D:Y.409 pi-Stacking: C:F.45, D:F.45, D:F.45, D:F.45

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: R.62, G.65, N.89, H.483, I.488, F.489, P.490 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.89, A:H.483 Water bridges: A:G.65, A:G.65, A:G.487 EDO.3: 11 residues within 4Å: Chain A: N.337, V.371, L.372, D.373, G.374, I.408, L.413, R.464, R.486 Ligands: YII.1, YII.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.337, A:V.371, A:R.486, A:R.486 EDO.5: 4 residues within 4Å: Chain A: N.337, R.338, R.462, Y.463 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.337, A:Y.463 EDO.19: 7 residues within 4Å: Chain B: R.62, G.65, N.89, H.483, I.488, F.489, P.490 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.89, B:H.483 Water bridges: B:G.65, B:G.65, B:G.487 EDO.20: 11 residues within 4Å: Chain B: N.337, V.371, L.372, D.373, G.374, I.408, L.413, R.464, R.486 Ligands: YII.1, YII.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.337, B:V.371, B:R.486, B:R.486 EDO.22: 4 residues within 4Å: Chain B: N.337, R.338, R.462, Y.463 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.337, B:Y.463 EDO.36: 7 residues within 4Å: Chain C: R.62, G.65, N.89, H.483, I.488, F.489, P.490 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.89 Water bridges: C:G.65, C:G.65, C:G.487 EDO.37: 11 residues within 4Å: Chain C: N.337, V.371, L.372, D.373, G.374, I.408, L.413, R.464, R.486 Ligands: YII.35, YII.52 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.337, C:V.371, C:R.486, C:R.486 EDO.39: 4 residues within 4Å: Chain C: N.337, R.338, R.462, Y.463 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.337, C:Y.463 EDO.53: 7 residues within 4Å: Chain D: R.62, G.65, N.89, H.483, I.488, F.489, P.490 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.89 Water bridges: D:G.65, D:G.65, D:G.487 EDO.54: 11 residues within 4Å: Chain D: N.337, V.371, L.372, D.373, G.374, I.408, L.413, R.464, R.486 Ligands: YII.35, YII.52 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.337, D:V.371, D:R.486, D:R.486 EDO.56: 4 residues within 4Å: Chain D: N.337, R.338, R.462, Y.463 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.337, D:Y.463

4 x OXL: OXALATE ION(Non-covalent)

OXL.4: 10 residues within 4Å: Chain A: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: SO4.15, MG.16 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.314, A:D.315, A:D.315, A:T.347, A:T.347, A:T.347 Water bridges: A:K.289, A:K.289 Salt bridges: A:R.92, A:K.289, A:K.289 OXL.21: 10 residues within 4Å: Chain B: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: SO4.32, MG.33 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.314, B:D.315, B:D.315, B:T.347, B:T.347, B:T.347 Water bridges: B:K.289, B:K.289 Salt bridges: B:R.92, B:K.289, B:K.289 OXL.38: 10 residues within 4Å: Chain C: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: SO4.49, MG.50 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.314, C:D.315, C:T.347, C:T.347 Water bridges: C:K.289, C:K.289 Salt bridges: C:R.92, C:K.289, C:K.289 OXL.55: 10 residues within 4Å: Chain D: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: SO4.66, MG.67 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.314, D:D.315, D:T.347, D:T.347 Water bridges: D:K.289, D:K.289 Salt bridges: D:R.92, D:K.289, D:K.289

40 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 8 residues within 4Å: Chain A: T.451, K.452, S.453, G.454, R.455, S.456, S.538, G.539 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: H.97, R.139 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: R.395, H.398, R.402 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: K.85, R.125 Ligands: SO4.10 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: K.85 Ligands: SO4.9 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: R.455, H.458, R.462 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: S.96, H.97, G.98 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: H.293, E.294, R.297 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: K.266, R.298 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain A: R.92, N.94, D.132, K.289 Ligands: OXL.4, MG.16 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain B: T.451, K.452, S.453, G.454, R.455, S.456, S.538, G.539 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain B: H.97, R.139 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: R.395, H.398, R.402 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain B: K.85, R.125 Ligands: SO4.27 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain B: K.85 Ligands: SO4.26 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: R.455, H.458, R.462 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: S.96, H.97, G.98 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain B: H.293, E.294, R.297 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain B: K.266, R.298 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain B: R.92, N.94, D.132, K.289 Ligands: OXL.21, MG.33 Ligand excluded by PLIP SO4.40: 8 residues within 4Å: Chain C: T.451, K.452, S.453, G.454, R.455, S.456, S.538, G.539 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain C: H.97, R.139 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain C: R.395, H.398, R.402 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain C: K.85, R.125 Ligands: SO4.44 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain C: K.85 Ligands: SO4.43 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain C: R.455, H.458, R.462 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain C: S.96, H.97, G.98 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain C: H.293, E.294, R.297 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain C: K.266, R.298 Ligand excluded by PLIP SO4.49: 6 residues within 4Å: Chain C: R.92, N.94, D.132, K.289 Ligands: OXL.38, MG.50 Ligand excluded by PLIP SO4.57: 8 residues within 4Å: Chain D: T.451, K.452, S.453, G.454, R.455, S.456, S.538, G.539 Ligand excluded by PLIP SO4.58: 2 residues within 4Å: Chain D: H.97, R.139 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain D: R.395, H.398, R.402 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain D: K.85, R.125 Ligands: SO4.61 Ligand excluded by PLIP SO4.61: 2 residues within 4Å: Chain D: K.85 Ligands: SO4.60 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain D: R.455, H.458, R.462 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain D: S.96, H.97, G.98 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain D: H.293, E.294, R.297 Ligand excluded by PLIP SO4.65: 2 residues within 4Å: Chain D: K.266, R.298 Ligand excluded by PLIP SO4.66: 6 residues within 4Å: Chain D: R.92, N.94, D.132, K.289 Ligands: OXL.55, MG.67 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 4 residues within 4Å: Chain A: E.291, D.315 Ligands: OXL.4, SO4.15 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.291, A:D.315, H2O.1, H2O.6 MG.33: 4 residues within 4Å: Chain B: E.291, D.315 Ligands: OXL.21, SO4.32 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.291, B:D.315, H2O.21, H2O.26 MG.50: 4 residues within 4Å: Chain C: E.291, D.315 Ligands: OXL.38, SO4.49 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.291, C:D.315, H2O.42, H2O.47 MG.67: 4 residues within 4Å: Chain D: E.291, D.315 Ligands: OXL.55, SO4.66 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.291, D:D.315, H2O.62, H2O.67

4 x NA: SODIUM ION(Non-functional Binders)

NA.17: 4 residues within 4Å: Chain A: E.437, K.441 Chain C: R.418, V.433 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.418 NA.34: 4 residues within 4Å: Chain B: E.437, K.441 Chain D: R.418, V.433 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.437 NA.51: 4 residues within 4Å: Chain A: R.418, V.433 Chain C: E.437, K.441 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.437, C:E.437 NA.68: 4 residues within 4Å: Chain B: R.418, V.433 Chain D: E.437, K.441 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.437, B:R.418

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wubben, T.J. et al., Development of Novel Small-Molecule Activators of Pyruvate Kinase Muscle Isozyme 2, PKM2, to Reduce Photoreceptor Apoptosis. Pharmaceuticals (2023)

Release Date

2023-05-17

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Pyruvate kinase PKM

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