MolNFT v1 · #161977 · protein
Crystal structure of KRAS-G12D in complex with gmp-pcp and compound 15R
6QUV · GTPase KRAS: “Crystal structure of KRAS-G12D in complex with gmp-pcp and compound 15R”. X-ray diffraction, 3 ligands (GCP, JJN, MG), 4 pockets (best druggability 0.69). MolNFT v1 #161977 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QUV
- 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, JJN, MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTPase KRAS | protein | 167 | 38% helix, 26% strand | P01116 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- JJN · (6~{a}~{R},11~{b}~{S})-6~{a}-(1,4-dimethylpiperidin-4-yl)-7,11~{b}-dihydro-6~{H}-indolo[2,3-c]isoquinolin-5-one · ligand · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.69 | 0.84 | 42 | GCP, MG |
| 2 | 221 | 0.64 | 0.83 | 38 | GCP, MG |
| 3 | 301 | 0.52 | 0.74 | 30 | JJN |
| 4 | 50 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 709 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6QUV · Crystal Structure of KRAS-G12D in complex with GMP-PCP and compound 15R · 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 6QUV · PDBe 6QUV · UniProt P01116
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