MolNFT v1 · #146894 · protein
SAMHD1 bound to cytarabine-tp in the catalytic pocket
6DW3 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “SAMHD1 bound to cytarabine-tp in the catalytic pocket”. X-ray diffraction, 4 ligands (HF4, DTP, GTP), 20 pockets (best druggability 0.89). MolNFT v1 #146894 on GenesisL1: 3D…
- PDB
- 6DW3
- Type
- protein
- Length
- 1,919 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- HF4, DTP, GTP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 13% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 51% helix, 13% strand | Q9Y3Z3 |
| B, A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- HF4 · 4-amino-1-{5-O-[(S)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one · ligand · 4 copies · chains D, C, B, A
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains D, C, B, A
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains D, C, A, B
- MG · Magnesium ion · metal · 8 copies · chains D, C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.89 | 0.92 | 119 | MG, DTP |
| 2 | 851 | 0.86 | 0.88 | 117 | DTP, MG, GTP |
| 3 | 669 | 0.85 | 0.89 | 81 | DTP, MG, GTP |
| 4 | 140 | 0.82 | 0.98 | 28 | empty |
| 5 | 134 | 0.81 | 0.98 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–A · 2207 Ų buried · 28 hydrogen bonds · protein-protein
- D–B · 2128 Ų buried · 31 hydrogen bonds · protein-protein
- D–A · 1946 Ų buried · 18 hydrogen bonds · protein-protein
- C–B · 1944 Ų buried · 17 hydrogen bonds · protein-protein
- B–A · 496 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6DW3 · SAMHD1 Bound to Cytarabine-TP in the Catalytic Pocket · the same entry in another collection · chain D against D, 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 Q9Y3Z3
- Elsewhere: RCSB PDB 6DW3 · PDBe 6DW3 · UniProt Q9Y3Z3
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