MolNFT v1 · #117647 · protein
GRB7 SH2 with bicyclic peptide inhibitor
5EEL · Growth factor receptor-bound protein 7: “GRB7 SH2 with bicyclic peptide inhibitor”. X-ray diffraction, 2 ligands (AEA, NA), 3 pockets (best druggability 0.45). MolNFT v1 #117647 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5EEL
- Type
- protein
- Length
- 675 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 7; Bicyclic peptide inhibitor
- UniProt
- Q14451
- Ligands
- AEA, NA
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 7 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Growth factor receptor-bound protein 7 | protein | 104 | 19% helix, 33% strand | Q14451 |
| B | Growth factor receptor-bound protein 7 | protein | 109 | 22% helix, 31% strand | Q14451 |
| C | Growth factor receptor-bound protein 7 | protein | 106 | 17% helix, 32% strand | Q14451 |
| D | Growth factor receptor-bound protein 7 | protein | 102 | 20% helix, 33% strand | Q14451 |
| E | Growth factor receptor-bound protein 7 | protein | 102 | 20% helix, 33% strand | Q14451 |
| F | Growth factor receptor-bound protein 7 | protein | 104 | 19% helix, 27% strand | Q14451 |
| L, M, N, P, Q, R | Bicyclic peptide inhibitor | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- AEA · (2-amino-2-carbamoyl-ethylsulfanyl)-acetic acid · ligand · 5 copies · chains C, F, L, M, B, N, Q, E, R
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 6 copies · chains A, B, C, D, E, F
- MLA · Malonic acid · additive · 5 copies · chains A, M, C, P, D, Q, E, R, F, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.45 | 0.76 | 23 | empty |
| 2 | 69 | 0.41 | 0.80 | 23 | FMT, NA |
| 3 | 55 | 0.34 | 0.78 | 16 | empty |
Interfaces
12 interfaces between chains.
- F–L · 482 Ų buried · 9 hydrogen bonds · protein-protein
- D–Q · 481 Ų buried · 9 hydrogen bonds · protein-protein
- E–R · 473 Ų buried · 8 hydrogen bonds · protein-protein
- C–P · 468 Ų buried · 9 hydrogen bonds · protein-protein
- B–N · 461 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent, 6 modified (covalent ligand, nonstandard).
Compared structures
- 5EEL · Grb7 SH2 with bicyclic peptide inhibitor · the same entry in another collection · chain R against R, 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 Q14451
- Elsewhere: RCSB PDB 5EEL · PDBe 5EEL · UniProt Q14451
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