MolNFT v1 · #135476 · protein
GRB7-SH2 with bicyclic peptide inhibitor containing a py mimetic
5U06 · Growth factor receptor-bound protein 7: “GRB7-SH2 with bicyclic peptide inhibitor containing a py mimetic”. X-ray diffraction, 2 ligands (48V, K), 4 pockets (best druggability 0.71). MolNFT v1 #135476 on GenesisL1: 3D structure…
- PDB
- 5U06
- Type
- protein
- Length
- 452 residues
- Chains
- 8
- 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
- 48V, K
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Growth factor receptor-bound protein 7 | protein | 107 | 18% helix, 32% strand | Q14451 |
| B | Growth factor receptor-bound protein 7 | protein | 102 | 18% helix, 34% strand | Q14451 |
| C | Growth factor receptor-bound protein 7 | protein | 108 | 19% helix, 32% strand | Q14451 |
| D | Growth factor receptor-bound protein 7 | protein | 103 | 17% helix, 29% strand | Q14451 |
| L, M, N, P | Bicyclic peptide inhibitor: lys-phe-glu-gly-cmf-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, P, B, M, C, N, D
- K · Potassium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.71 | 0.75 | 86 | 48V |
| 2 | 102 | 0.35 | 0.74 | 17 | empty |
| 3 | 71 | 0.32 | 0.75 | 18 | empty |
| 4 | 52 | 0.31 | 0.77 | 10 | empty |
Interfaces
13 interfaces between chains.
- C–D · 572 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 511 Ų buried · 15 hydrogen bonds · protein-protein
- B–M · 510 Ų buried · 16 hydrogen bonds · protein-protein
- D–P · 508 Ų buried · 12 hydrogen bonds · protein-protein
- C–N · 501 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 isopeptide, 4 modified (covalent ligand, isopeptide, nonstandard).
Compared structures
- 5U06 · Grb7-SH2 with bicyclic peptide inhibitor containing a pY mimetic · the same entry in another collection · chain P against P, TM-score 1.00
- Q14451 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 7 (Q14451) · a predicted model of the same protein · chain D 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 Q14451
- Elsewhere: RCSB PDB 5U06 · PDBe 5U06 · UniProt Q14451
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