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Structure of full length human ampk in complex with a small molecule activator, a benzimidazole derivative (991)

Analyse Structure of full length human ampk in complex with a small molecule activator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CFE
Type: protein
Length: 1,747 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-AMP-activated protein kinase catalytic subunit alpha-2; 5'-AMP-activated protein…
EC: 2.7.11.1, 2.7.11.27, 2.7.11.31
UniProt: P54646, Q9Y478, P54619
Ligands: AMP, STU, 992
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1, 2.7.11.27, 2.7.11.31)	protein	426	34% helix, 21% strand	P54646
B	5'-AMP-activated protein kinase subunit beta-1	protein	168	13% helix, 42% strand	Q9Y478
C	5'-AMP-activated protein kinase catalytic subunit alpha-2 (EC 2.7.11.1, 2.7.11.27, 2.7.11.31)	protein	404	34% helix, 22% strand	P54646
D	5'-AMP-activated protein kinase subunit beta-1	protein	167	11% helix, 42% strand	Q9Y478
E	5'-AMP-activated protein kinase subunit gamma-1	protein	294	37% helix, 23% strand	P54619
F	5'-AMP-activated protein kinase subunit gamma-1	protein	288	40% helix, 23% strand	P54619

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 6 copies · chains E, A, F, C
STU · Staurosporine · ligand · 2 copies · chains A, C
992 · 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid · ligand · 2 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1108	0.81	0.82	105	AMP
2	995	0.80	0.82	80	AMP
3	246	0.75	0.89	38	empty
4	925	0.75	0.78	75	empty
5	1003	0.72	0.76	69	empty

Interfaces

8 interfaces between chains.

C–D · 3764 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 3750 Å² buried · 36 hydrogen bonds · protein-protein
A–E · 1628 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 1472 Å² buried · 16 hydrogen bonds · protein-protein
B–E · 1214 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

4CFE · Structure of full length human AMPK in complex with a small molecule activator, a… · the same entry in another collection · chain F against F, TM-score 1.00
P54619 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma-1… · a predicted model of the same protein · chain F against A, TM-score 0.97
P54646 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase catalytic subunit… · a predicted model of the same protein · chain C against A, TM-score 0.97
Q9Y478 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-1… · a predicted model of the same protein · chain D against A, TM-score 0.90

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P54646
Every structure of UniProt Q9Y478
Every structure of UniProt P54619
Elsewhere: RCSB PDB 4CFE · PDBe 4CFE · UniProt P54646 · UniProt Q9Y478 · UniProt P54619

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