MolNFT v1 · #137022 · protein
Crystal structure of small molecule disulfide 2C07 bound to H-RAS M72C GDP
5VBE · GTPase HRAS: “Crystal structure of small molecule disulfide 2C07 bound to H-RAS M72C GDP”. X-ray diffraction, 3 ligands (GDP, 92V, MG), 2 pockets (best druggability 0.44). MolNFT v1 #137022 on GenesisL1: 3D structure, binding sites…
- PDB
- 5VBE
- Type
- protein
- Length
- 163 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS
- UniProt
- P01112
- Ligands
- GDP, 92V, MG
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 163 | 38% helix, 26% strand | P01112 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- 92V · 1-(4-methoxyphenyl)-N-(3-sulfanylpropyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.44 | 0.77 | 29 | GDP, MG |
| 2 | 99 | 0.43 | 0.78 | 16 | 92V |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5VBE · Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C GDP · the same entry in another collection · chain A against A, 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 P01112
- Elsewhere: RCSB PDB 5VBE · PDBe 5VBE · UniProt P01112
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