MolNFT v1 · #128009 · protein

Crystal structure of human pim-1 kinase in complex with a consensus peptide and fragment like molecule (E)-3-(2-(thiophen-2-YL)VINYL)-3, 4-dihydroquinoxalin-2(1H)-one

5NDT · SERINE/THREONINE-protein kinase pim-1: “Crystal structure of human pim-1 kinase in complex with a consensus peptide and fragment like molecule…”. X-ray diffraction, 1 ligand (8UB), 1 pocket (best druggability 0.70). MolNFT v1…

PDB: 5NDT
Type: protein
Length: 282 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase pim-1; Pimtide
EC: 2.7.11.1
UniProt: P11309
Ligands: 8UB
Pockets: 1 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 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	273	40% helix, 23% strand	P11309
B	Pimtide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

8UB · 3-(2-thiophen-2-ylethenyl)-1~{H}-quinoxalin-2-one · ligand · chains A
GOL · Glycerol · additive · 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	389	0.70	0.82	49	8UB

Interfaces

1 interface between chains.

A–B · 596 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5NDT · Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment… · 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 5NDT · PDBe 5NDT · UniProt P11309

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