Research workbench
Human gkrp bound to amg-0265 (N-[(R)-(2-CHLOROPHENYL){7-[4-(2- hydroxypropan-2-yl) pyridin-2-yl]-1-benzothiophen-2- YL}METHYL]CYCLOPROPANESULFONAMIDE) and sorbitol-6-phosphate
Analyse Human gkrp bound to amg-0265 (N-[(R)-(2-CHLOROPHENYL){7-[4-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PXS
- 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
- 2Y6, S6P, IOD, SO4
- Pockets
- 14 · best druggability 0.85
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 | 52% helix, 11% strand | Q14397 |
| B | Glucokinase regulatory protein | protein | 590 | 53% helix, 11% strand | Q14397 |
Ligands and binding sites
- 2Y6 · N-[(R)-(2-chlorophenyl){7-[4-(2-hydroxypropan-2-yl)pyridin-2-yl]-1-benzothiophen-2-yl}methyl]cyclopropanesulfonamide · ligand · 2 copies · chains A, B
- S6P · D-sorbitol-6-phosphate · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 29 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains B
- GOL · Glycerol · additive · 2 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.85 | 0.90 | 61 | 2Y6, S6P, IOD |
| 2 | 761 | 0.84 | 0.87 | 92 | 2Y6, S6P, IOD |
| 3 | 759 | 0.74 | 0.80 | 88 | IOD, SO4 |
| 4 | 149 | 0.55 | 0.81 | 32 | IOD, GOL |
| 5 | 87 | 0.51 | 0.83 | 15 | IOD |
Interfaces
1 interface between chains.
- A–B · 652 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4PXS · Human GKRP bound to AMG-0265 (N-[(R)-(2-CHLOROPHENYL){7-[4-(2-HYDROXYPROPAN-2-YL)… · 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 4PXS · PDBe 4PXS · UniProt Q14397
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