MolNFT v1 · #186870 · protein
Crystal structure of KRAS G12D with compound 24 (4-(4-[(1R,5S)-3,8- DIAZABICYCLO[3.2.1]OCTAN-3-yl]-8-fluoro-2-{[(2S,4S,7AR)-2- fluorotetrahydro-1H-pyrrolizin-7A(5H)-YL]METHOXY}PYRIDO[4,3- D]PYRIMIDIN-7-YL)NAPHTHALEN-2-ol) bound
7RT3 · Isoform 2B of GTPase KRAS: “Crystal structure of KRAS G12D with compound 24 (4-(4-[(1R,5S)-3,8…”. X-ray diffraction, 3 ligands (GDP, 7NZ, MG), 2 pockets (best druggability 0.72). MolNFT v1 #186870 on GenesisL1: 3D structure, binding…
- PDB
- 7RT3
- Type
- protein
- Length
- 168 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
- GDP, 7NZ, MG
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 168 | 38% helix, 25% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- 7NZ · 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2S,4S,7aR)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)naphthalen-2-ol · 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 | 193 | 0.72 | 0.89 | 24 | 7NZ |
| 2 | 127 | 0.50 | 0.80 | 26 | GDP, MG |
Compared structures
- 7RT3 · Crystal Structure of KRAS G12D with compound 24… · 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 7RT3 · PDBe 7RT3
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