MolNFT v1 · #100280 · protein

Human gkrp bound to amg-6861 and sorbitol-6-phosphate

4MSU · Glucokinase regulatory protein: “Human gkrp bound to amg-6861 and sorbitol-6-phosphate”. X-ray diffraction, 4 ligands (2EU, S6P, IOD), 16 pockets (best druggability 0.84). MolNFT v1 #100280 on GenesisL1: 3D structure, binding sites…

PDB: 4MSU
Type: protein
Length: 1,175 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucokinase regulatory protein
UniProt: Q14397
Ligands: 2EU, S6P, IOD, SO4
Pockets: 16 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucokinase regulatory protein	protein	585	52% helix, 10% strand	Q14397
B	Glucokinase regulatory protein	protein	590	54% helix, 11% strand	Q14397

Ligands and binding sites

2EU · 1,1,1,3,3,3-hexafluoro-2-{4-[4-(thiophen-2-ylsulfonyl)piperazin-1-yl]phenyl}propan-2-ol · ligand · 2 copies · chains A, B
S6P · D-sorbitol-6-phosphate · ligand · 2 copies · chains A, B
IOD · Iodide ion · ion · 23 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains B
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	593	0.84	0.89	69	2EU, S6P
2	634	0.84	0.88	70	2EU, S6P
3	772	0.74	0.79	93	IOD
4	59	0.60	0.91	15	IOD
5	163	0.55	0.81	38	IOD

Interfaces

1 interface between chains.

A–B · 654 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4MSU · Human GKRP bound to AMG-6861 and Sorbitol-6-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
Q14397 · AlphaFold monomer V2.0 prediction for glucokinase regulatory protein (Q14397) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q14397
Elsewhere: RCSB PDB 4MSU · PDBe 4MSU · UniProt Q14397

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