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Human PIM1 bound to benzothiophene inhibitor 379

Analyse Human PIM1 bound to benzothiophene inhibitor 379 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PDP
Type: protein
Length: 275 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase pim-1; Peptide
EC: 2.7.11.1
UniProt: P11309
Ligands: OBY, SO4
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 21% 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, 22% strand	P11309
B	Peptide	protein	7	0% helix, 0% strand	—

Ligands and binding sites

OBY · 5-[2-(acetylamino)-1-benzothiophen-4-yl]-N-cyclopropylthiophene-2-carboxamide · ligand · chains A
SO4 · Sulfate ion · ion · chains A

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	545	0.72	0.80	48	OBY
2	50	0.27	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 514 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6PDP · Human PIM1 bound to benzothiophene inhibitor 379 · 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 6PDP · PDBe 6PDP · UniProt P11309

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