MolNFT v1 · #101675 · protein
Approach for targeting RAS with small molecules that activate sos- mediated nucleotide exchange
4NYM · GTPase HRAS: “Approach for targeting RAS with small molecules that activate sos- mediated nucleotide exchange”. X-ray diffraction, 3 ligands (GNP, RND, MG), 11 pockets (best druggability 0.79). MolNFT v1 #101675 on GenesisL1: 3D…
- PDB
- 4NYM
- Type
- protein
- Length
- 801 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS; Son of sevenless homolog 1
- UniProt
- P01112, Q07889
- Ligands
- GNP, RND, MG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q | GTPase HRAS | protein | 166 | 36% helix, 26% strand | P01112 |
| R | GTPase HRAS | protein | 166 | 33% helix, 25% strand | P01112 |
| S | Son of sevenless homolog 1 | protein | 469 | 56% helix, 3% strand | Q07889 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Q
- RND · N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide · ligand · chains S
- MG · Magnesium ion · metal · chains Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.79 | 0.83 | 90 | GNP |
| 2 | 280 | 0.76 | 0.89 | 46 | empty |
| 3 | 53 | 0.66 | 0.95 | 16 | empty |
| 4 | 292 | 0.60 | 0.79 | 43 | empty |
| 5 | 196 | 0.49 | 0.76 | 30 | empty |
Interfaces
2 interfaces between chains.
- R–S · 1941 Ų buried · 29 hydrogen bonds · protein-protein
- Q–S · 1607 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4NYM · Approach for Targeting Ras with Small Molecules that Activate SOS-Mediated Nucleotide… · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q07889 · AlphaFold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889) · a predicted model of the same protein · chain S 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 P01112
- Every structure of UniProt Q07889
- Elsewhere: RCSB PDB 4NYM · PDBe 4NYM · UniProt P01112 · UniProt Q07889
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