MolNFT v1 · #52008 · protein

Structure of PKA complexed with 4-(4-chlorobenzyl)-1-(7H- PYRROLO(2,3-D)PYRIMIDIN-4-YL)PIPERIDIN-4-ylamine

2VO7 · Camp-dependent protein kinase, alpha-catalytic subunit: “Structure of PKA complexed with 4-(4-chlorobenzyl)-1-(7H- PYRROLO(2,3-D)PYRIMIDIN-4-YL)PIPERIDIN-4-ylamine”. X-ray diffraction, 1 ligand (M05), 6 pockets (best druggability…

PDB: 2VO7
Type: protein
Length: 357 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camp-dependent protein kinase, alpha-catalytic subunit; Camp-dependent protein kinase…
EC: 2.7.11.11
UniProt: P00517, P61925
Ligands: M05
Pockets: 6 · best druggability 0.80

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Camp-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11)	protein	337	37% helix, 16% strand	P00517
I	Camp-dependent protein kinase inhibitor alpha	protein	20	35% helix, 10% strand	P61925

Ligands and binding sites

M05 · 4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium · ligand · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	343	0.80	0.89	39	M05
2	108	0.44	0.78	18	empty
3	61	0.41	0.80	12	M05
4	74	0.32	0.74	16	empty
5	73	0.29	0.73	16	empty

Interfaces

1 interface between chains.

A–I · 1039 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

2VO7 · Structure of PKA complexed with 4-(4-Chlorobenzyl)-1-(7H-pyrrolo(2,3… · the same entry in another collection · chain A against A, TM-score 1.00
P61925 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain I against A, TM-score 0.40

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 P00517
Every structure of UniProt P61925
Elsewhere: RCSB PDB 2VO7 · PDBe 2VO7 · UniProt P00517 · UniProt P61925

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