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Exploitation of hydrogen bonding constraints and flat hydrophobic energy landscapes in pim-1 kinase needle screening and inhibitor design

Analyse Exploitation of hydrogen bonding constraints and flat hydrophobic energy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VBY
Type: protein
Length: 267 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: 0FR
Pockets: 3 · best druggability 0.64

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	267	40% helix, 23% strand	P11309

Ligands and binding sites

0FR · furan-2-yl(1H-indol-3-yl)methanone · ligand · chains A
IMD · Imidazole · additive · 2 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.64	0.83	28	0FR
2	88	0.49	0.83	19	empty
3	56	0.34	0.77	9	empty

Compared structures

3VBY · Exploitation of hydrogen bonding constraints and flat hydrophobic energy landscapes in… · 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 3VBY · PDBe 3VBY · UniProt P11309

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