MolNFT v1 · #150083 · protein
Crystal structure of KRAS G12D (gppcp) in complex with 15
6GJ5 · GTPase KRAS: “Crystal structure of KRAS G12D (gppcp) in complex with 15”. X-ray diffraction, 3 ligands (GCP, F0N, MG), 4 pockets (best druggability 0.60). MolNFT v1 #150083 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6GJ5
- Type
- protein
- Length
- 325 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GCP, F0N, MG
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 163 | 37% helix, 28% strand | P01116 |
| B | GTPase KRAS | protein | 162 | 36% helix, 28% strand | P01116 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- F0N · (3~{S})-3-[2-[(2~{R})-pyrrolidin-2-yl]-1~{H}-indol-3-yl]-2,3-dihydroisoindol-1-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.60 | 0.82 | 21 | empty |
| 2 | 182 | 0.58 | 0.81 | 31 | GCP, MG |
| 3 | 174 | 0.54 | 0.80 | 30 | GCP, MG |
| 4 | 71 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 566 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GJ5 · Crystal structure of KRAS G12D (gppcp) in complex with 15 · 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 P01116
- Elsewhere: RCSB PDB 6GJ5 · PDBe 6GJ5 · UniProt P01116
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