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Human PIM1 bound to benzothiophene inhibitor 354

Analyse Human PIM1 bound to benzothiophene inhibitor 354 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PDO
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: OD1
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase pim-1 (EC 2.7.11.1)	protein	267	39% helix, 22% strand	P11309
B	Peptide	protein	8	0% helix, 0% strand	—

Ligands and binding sites

OD1 · 4-{5-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxamide · ligand · chains A, B

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	419	0.65	0.79	45	OD1

Interfaces

1 interface between chains.

A–B · 537 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6PDO · Human PIM1 bound to benzothiophene inhibitor 354 · 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 6PDO · PDBe 6PDO · UniProt P11309

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