MolNFT v1 · #126197 · protein

Human PDK1 kinase domain in complex with adenosine bound to the ATP- binding site

5LVN · 3-phosphoinositide-dependent protein kinase 1: “Human PDK1 kinase domain in complex with adenosine bound to the ATP- binding site”. X-ray diffraction, 2 ligands (ADN, CL), 1 pocket (best druggability 0.65). MolNFT v1 #126197 on…

PDB: 5LVN
Type: protein
Length: 284 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-phosphoinositide-dependent protein kinase 1
EC: 2.7.11.1
UniProt: O15530
Ligands: ADN, CL
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1)	protein	284	40% helix, 18% strand	O15530

Ligands and binding sites

ADN · Adenosine · ligand · chains A
CL · Chloride ion · ion · chains A
DTD · Dithiane diol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	383	0.65	0.79	39	ADN

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

5LVN · Human PDK1 Kinase Domain in Complex with Adenosine Bound to the ATP-Binding Site · the same entry in another collection · chain A against A, TM-score 1.00

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 O15530
Elsewhere: RCSB PDB 5LVN · PDBe 5LVN · UniProt O15530

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