Research workbench
Crystal structure of KRAS-G12D in complex with natural product-like compound 9B
Analyse Crystal structure of KRAS-G12D in complex with natural product-like compound 9B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QUW
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GCP, JJQ, MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTPase KRAS | protein | 167 | 40% helix, 26% strand | P01116 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- JJQ · (3~{a}~{R},8~{b}~{S})-2,2,3~{a},8~{b}-tetramethyl-3,4-dihydro-1~{H}-pyrrolo[2,3-b]indole · ligand · chains 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 | 253 | 0.67 | 0.84 | 39 | GCP, MG |
| 2 | 209 | 0.64 | 0.84 | 36 | GCP, MG |
| 3 | 239 | 0.50 | 0.75 | 29 | JJQ |
| 4 | 60 | 0.32 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 686 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6QUW · Crystal Structure of KRAS-G12D in Complex with Natural Product-Like Compound 9b · the same entry in another collection · chain B against B, 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 6QUW · PDBe 6QUW · UniProt P01116
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