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Crystal structure of human PDK2 complexed with an allosteric inhibitor compound 8C

Analyse Crystal structure of human PDK2 complexed with an allosteric inhibitor compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LIL
Type: protein
Length: 690 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
EC: 2.7.11.2
UniProt: Q15119
Ligands: EGX, SO4
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	[pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2)	protein	346	54% helix, 15% strand	Q15119
B	[pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2)	protein	344	54% helix, 15% strand	Q15119

Ligands and binding sites

EGX · 1-(1-piperidin-4-ylpyrazol-4-yl)anthracene-9,10-dione · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · chains A
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
FLC · Citrate anion · additive · 2 copies · chains A, B
GOL · Glycerol · additive · chains A

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	425	0.71	0.82	55	FLC, PEG
2	425	0.70	0.81	51	FLC, PEG
3	108	0.65	0.89	19	EGX
4	99	0.65	0.89	16	EGX
5	372	0.64	0.79	38	empty

Interfaces

1 interface between chains.

A–B · 1229 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6LIL · Crystal structure of human PDK2 complexed with an allosteric inhibitor compound 8c · the same entry in another collection · chain B against B, TM-score 1.00
Q15119 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q15119
Elsewhere: RCSB PDB 6LIL · PDBe 6LIL · UniProt Q15119

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