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Crystal structure of PIM1 with inhibitor: 2-pyridin-3-yl-1~{H}- benzimidazole

Analyse Crystal structure of PIM1 with inhibitor: 2-pyridin-3-yl-1~{H}- benzimidazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KGD
Type: protein
Length: 273 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: 6SL, SO4
Pockets: 1 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase pim-1 (EC 2.7.11.1)	protein	273	40% helix, 23% strand	P11309

Ligands and binding sites

6SL · 2-pyridin-3-yl-1~{H}-benzimidazole · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 19 copies · 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	375	0.70	0.82	47	EDO, 6SL

Compared structures

5KGD · Crystal structure of PIM1 with inhibitor: 2-pyridin-3-yl-1~{H}-benzimidazole · 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 P11309
Elsewhere: RCSB PDB 5KGD · PDBe 5KGD · UniProt P11309

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