MolNFT v1 · #172761 · protein
Crystal structure of inactive KRAS G12D (GDP) in complex with the soaked dimeric inhibitor bi-5747
7ACQ · GTPase KRAS: “Crystal structure of inactive KRAS G12D (GDP) in complex with the soaked dimeric inhibitor bi-5747”. X-ray diffraction, 3 ligands (GDP, R6W, MG), 5 pockets (best druggability 0.69). MolNFT v1 #172761 on GenesisL1: 3D…
- PDB
- 7ACQ
- Type
- protein
- Length
- 487 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- EC
- 3.6.5.2
- UniProt
- P01116
- Ligands
- GDP, R6W, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS (EC 3.6.5.2) | protein | 164 | 38% helix, 26% strand | P01116 |
| B | GTPase KRAS (EC 3.6.5.2) | protein | 163 | 37% helix, 25% strand | P01116 |
| C | GTPase KRAS (EC 3.6.5.2) | protein | 160 | 38% helix, 26% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- R6W · (3~{S})-5-oxidanyl-3-[2-[[6-[[3-[(1~{S})-6-oxidanyl-3-oxidanylidene-1,2-dihydroisoindol-1-yl]-1~{H}-indol-2-yl]methylamino]hexylamino]methyl]-1~{H}-indol-3-yl]-2, 3-dihydroisoindol-1-one · ligand · 2 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.69 | 0.78 | 55 | R6W |
| 2 | 151 | 0.54 | 0.80 | 22 | empty |
| 3 | 138 | 0.48 | 0.78 | 27 | GDP, MG |
| 4 | 118 | 0.44 | 0.77 | 26 | GDP, MG |
| 5 | 118 | 0.42 | 0.76 | 27 | GDP, MG |
Interfaces
3 interfaces between chains.
- B–C · 286 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 212 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7ACQ · Crystal structure of inactive KRAS G12D (GDP) in complex with the soaked dimeric… · 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 7ACQ · PDBe 7ACQ · UniProt P01116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.