Research workbench
Crystal structure of KRAS G12D with compound 15 (4-(4-[(1R,5S)-3,8- DIAZABICYCLO[3.2.1]OCTAN-3-yl]-8-fluoro-2-{[(2S)-1-methylpyrrolidin- 2-YL]METHOXY}PYRIDO[4,3-D]PYRIMIDIN-7-YL)NAPHTHALEN-2-ol) bound
Analyse Crystal structure of KRAS G12D with compound 15 (4-(4-[(1R,5S)-3,8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RT1
- Type
- protein
- Length
- 169 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2B of GTPase KRAS
- EC
- 3.6.5.2
- Ligands
- 7L8, GDP, MG
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 169 | 37% helix, 25% strand | — |
Ligands and binding sites
- 7L8 · 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)naphthalen-2-ol · ligand · 2 copies · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.68 | 0.88 | 23 | 7L8 |
| 2 | 120 | 0.46 | 0.79 | 26 | GDP, MG |
Compared structures
- 7RT1 · Crystal Structure of KRAS G12D with compound 15… · 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 7RT1 · PDBe 7RT1
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