MolNFT v1 · #177862 · protein
GDP-bound KRAS G12D in complex with th-Z827
7EWA · Isoform 2B of GTPase KRAS: “GDP-bound KRAS G12D in complex with th-Z827”. X-ray diffraction, 4 ligands (05F, GNP, GDP), 6 pockets (best druggability 0.80). MolNFT v1 #177862 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7EWA
- Type
- protein
- Length
- 490 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2B of GTPase KRAS
- EC
- 3.6.5.2
- UniProt
- P01116
- Ligands
- 05F, GNP, GDP, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 169 | 37% helix, 25% strand | P01116 |
| C | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 152 | 38% helix, 26% strand | P01116 |
Ligands and binding sites
- 05F · 4-[(1~{R},5~{S})-3,8-diazabicyclo[3.2.1]octan-8-yl]-7-(8-methylnaphthalen-1-yl)-2-[[(2~{S})-1-methylpyrrolidin-2-yl]methoxy]-6,8-dihydro-5~{H}-pyrido[3,4-d]pyrimidine · ligand · 2 copies · chains A, B
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains B, C
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.80 | 0.82 | 67 | empty |
| 2 | 323 | 0.72 | 0.85 | 45 | MG, 05F, GNP |
| 3 | 191 | 0.71 | 0.88 | 23 | 05F |
| 4 | 125 | 0.49 | 0.80 | 25 | empty |
| 5 | 136 | 0.47 | 0.78 | 27 | MG, GDP |
Interfaces
3 interfaces between chains.
- A–B · 607 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 399 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 333 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7EWA · GDP-bound KRAS G12D in complex with TH-Z827 · 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 7EWA · PDBe 7EWA · UniProt P01116
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