SMTL ID : 6e4w.2 (1 other biounit)

Structure of AMPK bound to activator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x STU: STAUROSPORINE(Non-covalent)

STU.1: 18 residues within 4Å: Chain A: L.24, G.25, V.26, G.27, V.32, A.45, I.79, M.95, E.96, Y.97, V.98, G.101, E.102, E.145, N.146, L.148, A.158, D.159 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.24, A:L.24, A:V.32, A:V.32, A:A.45, A:Y.97, A:E.102, A:L.148, A:L.148 Hydrogen bonds: A:V.98, A:E.145 STU.10: 18 residues within 4Å: Chain D: L.24, G.25, V.26, G.27, V.32, A.45, I.79, M.95, E.96, Y.97, V.98, G.101, E.102, E.145, N.146, L.148, A.158, D.159 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.24, D:L.24, D:V.32, D:V.32, D:A.45, D:Y.97, D:E.102, D:L.148, D:L.148 Hydrogen bonds: D:V.98, D:E.145

2 x HUG: 1-O-(4,6-difluoro-5-{4-[(2S)-oxan-2-yl]phenyl}-1H-indole-3-carbonyl)-beta-D-glucopyranuronic acid(Non-covalent)

HUG.2: 19 residues within 4Å: Chain A: V.13, L.20, G.21, K.31, K.33, I.48, N.50, K.53, D.90, F.92 Chain B: V.15, R.17, T.19, T.40, S.42, N.44, N.45, V.47, I.49 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:V.13, A:L.20, A:K.33, A:I.48, B:T.40, B:V.47 Hydrogen bonds: A:D.90, B:N.44, B:N.45 Salt bridges: A:K.31, A:K.31, B:R.17, B:R.17 Halogen bonds: A:K.31 pi-Cation interactions: B:R.17 HUG.11: 19 residues within 4Å: Chain D: V.13, L.20, G.21, K.31, K.33, I.48, N.50, K.53, D.90, F.92 Chain E: V.15, R.17, T.19, T.40, S.42, N.44, N.45, V.47, I.49 15 PLIP interactions: 8 interactions with chain D, 7 interactions with chain E Hydrophobic interactions: D:V.13, D:L.20, D:K.33, D:I.48, E:T.40, E:V.47 Hydrogen bonds: D:D.90, E:N.44, E:N.45 Salt bridges: D:K.31, D:K.31, E:R.17, E:R.17 Halogen bonds: D:K.31 pi-Cation interactions: E:R.17

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: S.99, A.151 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: V.26 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.36, K.43 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain D: S.99, A.151 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain D: V.26 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain D: K.36, K.43 Ligand excluded by PLIP

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 13 residues within 4Å: Chain C: H.150, T.199, I.203, A.204, V.224, S.225, A.226, P.228, R.298, I.311, S.313, S.315, D.316 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.199, C:A.204, C:A.204, C:S.225, C:R.298, C:S.313, C:S.315, C:D.316 Salt bridges: C:H.150 AMP.7: 11 residues within 4Å: Chain C: R.69, I.239, S.241, F.243, D.244, R.268, L.276, V.296, H.297, R.298, V.300 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.241, C:F.243, C:D.244, C:L.276, C:L.276, C:H.297, C:R.298 Salt bridges: C:R.69, C:H.297, C:R.298 AMP.15: 13 residues within 4Å: Chain F: H.150, T.199, I.203, A.204, V.224, S.225, A.226, P.228, R.298, I.311, S.313, S.315, D.316 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:T.199, F:T.199, F:A.204, F:A.204, F:S.225, F:R.298, F:S.313, F:S.315, F:D.316 Salt bridges: F:H.150 AMP.16: 11 residues within 4Å: Chain F: R.69, I.239, S.241, F.243, D.244, R.268, L.276, V.296, H.297, R.298, V.300 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:S.241, F:F.243, F:D.244, F:L.276, F:H.297, F:R.298 Salt bridges: F:R.69, F:H.297, F:R.298

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.8: 15 residues within 4Å: Chain C: R.69, M.84, T.86, I.87, T.88, D.89, Y.120, P.127, L.128, V.129, I.149, H.150, R.151, P.153, K.242 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:I.87, C:T.88, C:D.89, C:Y.120, C:Y.120, C:V.129, C:V.129, C:H.150, C:R.151 Salt bridges: C:R.69, C:H.150, C:H.150, C:R.151, C:K.242, C:K.242 ADP.17: 15 residues within 4Å: Chain F: R.69, M.84, T.86, I.87, T.88, D.89, Y.120, P.127, L.128, V.129, I.149, H.150, R.151, P.153, K.242 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:T.86, F:I.87, F:T.88, F:D.89, F:Y.120, F:V.129, F:V.129, F:H.150, F:R.151 Salt bridges: F:R.69, F:H.150, F:H.150, F:R.151, F:K.242, F:K.242

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

SO4.9: 4 residues within 4Å: Chain C: R.151, T.167, K.169, H.297 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.167 Salt bridges: C:R.151, C:H.297 SO4.18: 4 residues within 4Å: Chain F: R.151, T.167, K.169, H.297 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.167, F:T.167 Salt bridges: F:R.151, F:H.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ryder, T.F. et al., Acyl Glucuronide Metabolites of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1 H-indole-3-carboxylic Acid (PF-06409577) and Related Indole-3-carboxylic Acid Derivatives are Direct Activators of Adenosine Monophosphate-Activated Protein Kinase (AMPK). J. Med. Chem. (2018)

Release Date

2018-08-08

Peptides

5'-AMP-activated protein kinase catalytic subunit alpha-1: AD
5'-AMP-activated protein kinase subunit beta-1: BE
5'-AMP-activated protein kinase subunit gamma-1: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
C

F
C

5'-AMP-activated protein kinase catalytic subunit alpha-1

5'-AMP-activated protein kinase subunit beta-1

5'-AMP-activated protein kinase subunit gamma-1

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