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Crystal structure of pim-1 in complex with the fluorescent compound SKF86002

Analyse Crystal structure of pim-1 in complex with the fluorescent compound SKF86002 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LL5
Type: protein
Length: 268 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: SK8, CA
Pockets: 3 · best druggability 0.73

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase pim-1 (EC 2.7.11.1)	protein	268	39% helix, 23% strand	P11309

Ligands and binding sites

SK8 · 6-(4-fluorophenyl)-5-(pyridin-4-yl)-2,3-dihydroimidazo[2,1-b][1,3]thiazole · ligand · chains A
CA · Calcium ion · metal · chains A
GOL · Glycerol · additive · 4 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	57	0.73	0.98	22	empty
2	232	0.64	0.82	28	SK8
3	117	0.51	0.81	24	GOL

Compared structures

4LL5 · Crystal Structure of Pim-1 in complex with the fluorescent compound SKF86002 · the same entry in another collection · chain A against A, TM-score 1.00

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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 4LL5 · PDBe 4LL5 · UniProt P11309

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