MolNFT v1 · #128624 · protein
Crystal structure of TNKS2 in complex with 2-[4-(DIETHYLAMINO)PHENYL]- 3,4-dihydroquinazolin-4-one
5NWD · Tankyrase-2: “Crystal structure of TNKS2 in complex with 2-[4-(DIETHYLAMINO)PHENYL]- 3,4-dihydroquinazolin-4-one”. X-ray diffraction, 3 ligands (9C8, ZN, SO4), 4 pockets (best druggability 0.81). MolNFT v1 #128624 on GenesisL1: 3D…
- PDB
- 5NWD
- Type
- protein
- Length
- 417 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tankyrase-2
- EC
- 2.4.2.30
- UniProt
- Q9H2K2
- Ligands
- 9C8, ZN, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-2 (EC 2.4.2.30) | protein | 161 | 29% helix, 25% strand | Q9H2K2 |
| H, I | Tankyrase-2 (EC 2.4.2.30) | protein | 47 | 6% helix, 45% strand | Q9H2K2 |
| B | Tankyrase-2 (EC 2.4.2.30) | protein | 162 | 29% helix, 25% strand | Q9H2K2 |
Ligands and binding sites
- 9C8 · 2-[4-(diethylamino)phenyl]-3~{H}-quinazolin-4-one · ligand · 2 copies · chains A, H, B, I
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, H, B, I
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.81 | 0.88 | 58 | 9C8, SO4 |
| 2 | 218 | 0.64 | 0.83 | 38 | 9C8, SO4 |
| 3 | 127 | 0.50 | 0.80 | 18 | empty |
| 4 | 105 | 0.37 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–H · 3078 Ų buried · 65 hydrogen bonds · protein-protein
- B–I · 3062 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 585 Ų buried · 4 hydrogen bonds · protein-protein
- A–I · 98 Ų buried · 0 hydrogen bonds · protein-protein
- H–B · 55 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NWD · Crystal structure of TNKS2 in complex with 2-[4-(diethylamino)phenyl]-3,4-dihydroquinazoli… · 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 Q9H2K2
- Elsewhere: RCSB PDB 5NWD · PDBe 5NWD · UniProt Q9H2K2
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