MolNFT v1 · #102427 · protein

Human gkrp bound to AMG5106 and sorbitol-6-phosphate

4OLH · Glucokinase regulatory protein: “Human gkrp bound to AMG5106 and sorbitol-6-phosphate”. X-ray diffraction, 4 ligands (2TO, S6P, IOD), 14 pockets (best druggability 0.79). MolNFT v1 #102427 on GenesisL1: 3D structure, binding sites…

PDB: 4OLH
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: 2TO, S6P, IOD, SO4
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucokinase regulatory protein	protein	585	53% helix, 11% strand	Q14397
B	Glucokinase regulatory protein	protein	590	53% helix, 11% strand	Q14397

Ligands and binding sites

2TO · 2-(2-{4-[(6-aminopyridin-3-yl)sulfonyl]piperazin-1-yl}-3,3'-bipyridin-5-yl)-1,1,1,3,3,3-hexafluoropropan-2-ol · ligand · 2 copies · chains A, B
S6P · D-sorbitol-6-phosphate · ligand · 2 copies · chains A, B
IOD · Iodide ion · ion · 27 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains B
GOL · Glycerol · additive · chains B

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	193	0.79	0.94	37	S6P
2	448	0.78	0.86	38	2TO, IOD
3	454	0.78	0.86	39	2TO, IOD
4	317	0.76	0.88	57	S6P, IOD, GOL
5	856	0.75	0.79	97	IOD

Interfaces

1 interface between chains.

A–B · 670 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4OLH · Human GKRP Bound to AMG5106 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 4OLH · PDBe 4OLH · UniProt Q14397

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