MolNFT v1 · #172753 · protein
Crystal structure of active KRAS G12D (gppcp) in complex with the soaked dimeric inhibitor bi-5747
7ACH · GTPase KRAS: “Crystal structure of active KRAS G12D (gppcp) in complex with the soaked dimeric inhibitor bi-5747”. X-ray diffraction, 3 ligands (GCP, R6W, MG), 4 pockets (best druggability 0.66). MolNFT v1 #172753 on GenesisL1: 3D…
- PDB
- 7ACH
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- EC
- 3.6.5.2
- UniProt
- P01116
- Ligands
- GCP, R6W, MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTPase KRAS (EC 3.6.5.2) | protein | 167 | 38% helix, 26% strand | P01116 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- 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 · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.66 | 0.83 | 41 | GCP, MG |
| 2 | 206 | 0.63 | 0.83 | 37 | GCP, MG |
| 3 | 249 | 0.50 | 0.75 | 28 | R6W |
| 4 | 63 | 0.32 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 712 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7ACH · Crystal structure of active KRAS G12D (gppcp) 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 7ACH · PDBe 7ACH · UniProt P01116
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