MolNFT v1 · #152771 · protein
Phosphoglycerate mutase 1 complexed with a small molecule inhibitor
6ISN: “Phosphoglycerate mutase 1 complexed with a small molecule inhibitor”. X-ray diffraction, 2 ligands (AW6, CL), 5 pockets (best druggability 0.63). MolNFT v1 #152771 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ISN
- Type
- protein
- Length
- 467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase 1
- EC
- 5.4.2.11, 5.4.2.4
- UniProt
- P18669
- Ligands
- AW6, CL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Phosphoglycerate mutase 1 (EC 5.4.2.11, 5.4.2.4) | protein | 233 | 45% helix, 12% strand | P18669 |
| C | Phosphoglycerate mutase 1 (EC 5.4.2.11, 5.4.2.4) | protein | 234 | 44% helix, 15% strand | P18669 |
Ligands and binding sites
- AW6 · 4-chloro-N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)benzene-1-sulfonamide · ligand · chains C
- CL · Chloride ion · ion · chains B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.63 | 0.78 | 35 | MES, AW6 |
| 2 | 274 | 0.58 | 0.78 | 33 | empty |
| 3 | 120 | 0.43 | 0.77 | 14 | empty |
| 4 | 153 | 0.43 | 0.74 | 19 | empty |
| 5 | 144 | 0.42 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- B–C · 1070 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6ISN · Phosphoglycerate mutase 1 complexed with a small molecule inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
- P18669 · AlphaFold monomer V2.0 prediction for phosphoglycerate mutase 1 (P18669) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P18669
- Elsewhere: RCSB PDB 6ISN · PDBe 6ISN · UniProt P18669
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