Research workbench

Protein kinase a in complex with an inhibitor

Analyse Protein kinase a in complex with an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UJ9
Type: protein
Length: 360 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camp-dependent protein kinase catalytic subunit alpha; Peptide
EC: 2.7.11.11
UniProt: P17612
Ligands: TPO, S3N
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11)	protein	340	37% helix, 16% strand	P17612
B	Peptide	protein	20	35% helix, 10% strand	—

Ligands and binding sites

TPO · Phosphothreonine · ligand · chains A, B
S3N · 7-[(3S,4R)-4-[4-(trifluoromethyl)phenyl]carbonylpyrrolidin-3-yl]-3H-quinazolin-4-one · ligand · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	334	0.79	0.89	41	S3N
2	216	0.53	0.77	33	MPD
3	100	0.45	0.80	20	empty
4	56	0.32	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 1060 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 modified (covalent ligand, phosphorylation).

Compared structures

4UJ9 · Protein Kinase A in complex with an Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P17612 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · 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 P17612
Elsewhere: RCSB PDB 4UJ9 · PDBe 4UJ9 · UniProt P17612

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