MolNFT v1 · #135528 · protein
GRB7-SH2 with bicyclic peptide inhibitor
5U1Q · Growth factor receptor-bound protein 7: “GRB7-SH2 with bicyclic peptide inhibitor”. X-ray diffraction, 2 ligands (48V, CL), 3 pockets (best druggability 0.68). MolNFT v1 #135528 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5U1Q
- Type
- protein
- Length
- 445 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth factor receptor-bound protein 7; Lys-phe-glu-gly-tyr-asp-asn-glu-cst
- UniProt
- Q14451
- Ligands
- 48V, CL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Growth factor receptor-bound protein 7 | protein | 100 | 18% helix, 34% strand | Q14451 |
| B | Growth factor receptor-bound protein 7 | protein | 107 | 21% helix, 32% strand | Q14451 |
| C | Growth factor receptor-bound protein 7 | protein | 105 | 21% helix, 35% strand | Q14451 |
| D | Growth factor receptor-bound protein 7 | protein | 101 | 18% helix, 32% strand | Q14451 |
| L, M, N, P | Lys-phe-glu-gly-tyr-asp-asn-glu-cst | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · 4 copies · chains A, L, B, M, C, N, D, P
- CL · Chloride ion · ion · 4 copies · chains A, L, B, D, P, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.68 | 0.74 | 69 | empty |
| 2 | 116 | 0.45 | 0.78 | 18 | empty |
| 3 | 108 | 0.44 | 0.78 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–B · 454 Ų buried · 7 hydrogen bonds · protein-protein
- D–P · 451 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 445 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 422 Ų buried · 3 hydrogen bonds · protein-protein
- C–N · 410 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 isopeptide (covalent ligand, isopeptide).
Compared structures
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 5U1Q · PDBe 5U1Q · UniProt Q14451
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.