MolNFT v1 · #137622 · protein

PIM1 kinase in complex with a benzofuranone inhibitor

5VUB · SERINE/THREONINE-protein kinase pim-1: “PIM1 kinase in complex with a benzofuranone inhibitor”. X-ray diffraction, 1 ligand (8GU), 2 pockets (best druggability 0.60). MolNFT v1 #137622 on GenesisL1: 3D structure, binding sites and…

PDB: 5VUB
Type: protein
Length: 270 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase pim-1
EC: 2.7.11.1
UniProt: P11309
Ligands: 8GU
Pockets: 2 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	SERINE/THREONINE-protein kinase pim-1 (EC 2.7.11.1)	protein	270	39% helix, 23% strand	P11309

Ligands and binding sites

8GU · (2Z)-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1H-pyrrolo[3,2-b]pyridin-3-ylmethylidene)-1-benzofuran-3-one · ligand · chains B
GOL · Glycerol · additive · chains B

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

Pockets

2 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	245	0.60	0.80	29	8GU
2	113	0.48	0.80	22	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

5VUB · Pim1 Kinase in complex with a benzofura inhibitor · the same entry in another collection · chain B against B, 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 P11309
Elsewhere: RCSB PDB 5VUB · PDBe 5VUB · UniProt P11309

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