MolNFT v1 · #191416 · protein
Crystal structure of human KRAS G12C covalently bound with astrazeneca WO2020/178282A1 compound 76
8DNJ · Isoform 2B of GTPase KRAS: “Crystal structure of human KRAS G12C covalently bound with astrazeneca WO2020/178282A1 compound 76”. X-ray diffraction, 3 ligands (GDP, U4U, MG), 6 pockets (best druggability 0.68). MolNFT v1 #191416 on…
- PDB
- 8DNJ
- Type
- protein
- Length
- 506 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
- Ligands
- GDP, U4U, MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 170 | 37% helix, 25% strand | — |
| B | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 168 | 38% helix, 24% strand | — |
| C | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 168 | 36% helix, 26% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- U4U · 1-[(5s,9p,12ar)-9-(2-chloro-6-hydroxyphenyl)-8-ethynyl-10-fluoro-3,4,12,12A-tetrahydro-6H-pyrazino[2,1-C][1, 4]benzoxazepin-2(1H)-yl]propan-1-one · ligand · 3 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
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 | 346 | 0.68 | 0.82 | 41 | MG, GDP, U4U |
| 2 | 386 | 0.65 | 0.79 | 47 | MG, GDP, U4U |
| 3 | 318 | 0.64 | 0.80 | 41 | MG, GDP, U4U |
| 4 | 131 | 0.39 | 0.74 | 19 | empty |
| 5 | 118 | 0.34 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 585 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 8DNJ · Crystal structure of human KRAS G12C covalently bound with AstraZeneca WO2020/178282A1… · 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
- Elsewhere: RCSB PDB 8DNJ · PDBe 8DNJ
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