Research workbench
GDP-bound KRAS G12D in complex with TH-Z816
Analyse GDP-bound KRAS G12D in complex with TH-Z816 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EW9
- Type
- protein
- Length
- 501 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.13
- Source
- Homo sapiens
- Molecule
- Isoform 2B of GTPase KRas
- EC
- 3.6.5.2
- UniProt
- P01116
- Ligands
- GDP, 05C, MG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.13 · 3 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2B of GTPase KRas (EC 3.6.5.2) | protein | 168 | 37% helix, 26% strand | P01116 |
| B | Isoform 2B of GTPase KRas (EC 3.6.5.2) | protein | 169 | 36% helix, 25% strand | P01116 |
| C | Isoform 2B of GTPase KRas (EC 3.6.5.2) | protein | 164 | 34% helix, 27% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- 05C · 7-(8-methylnaphthalen-1-yl)-4-[(2~{R})-2-methylpiperazin-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
- 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.82 | 0.83 | 76 | empty |
| 2 | 182 | 0.73 | 0.90 | 23 | 05C |
| 3 | 341 | 0.73 | 0.85 | 43 | MG, 05C, GDP |
| 4 | 196 | 0.55 | 0.79 | 27 | empty |
| 5 | 134 | 0.47 | 0.78 | 26 | MG, GDP |
Interfaces
3 interfaces between chains.
- A–B · 594 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 349 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7EW9 · GDP-bound KRAS G12D in complex with th-Z816 · 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 7EW9 · PDBe 7EW9 · UniProt P01116
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