MolNFT v1 · #128589 · protein
Crystal structure of TNKS2 in complex with 2-(3-hydroxyphenyl)-3,4- dihydroquinazolin-4-one
5NVC · Tankyrase-2: “Crystal structure of TNKS2 in complex with 2-(3-hydroxyphenyl)-3,4- dihydroquinazolin-4-one”. X-ray diffraction, 3 ligands (9AN, ZN, SO4), 4 pockets (best druggability 0.82). MolNFT v1 #128589 on GenesisL1: 3D…
- PDB
- 5NVC
- 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
- 9AN, ZN, SO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-2 (EC 2.4.2.30) | protein | 161 | 29% helix, 25% strand | Q9H2K2 |
| C, D | Tankyrase-2 (EC 2.4.2.30) | protein | 47 | 6% helix, 43% strand | Q9H2K2 |
| B | Tankyrase-2 (EC 2.4.2.30) | protein | 162 | 29% helix, 25% strand | Q9H2K2 |
Ligands and binding sites
- 9AN · 2-(3-hydroxyphenyl)-3~{H}-quinazolin-4-one · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · chains C
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 | 491 | 0.82 | 0.89 | 61 | SO4, 9AN |
| 2 | 256 | 0.65 | 0.82 | 40 | SO4, 9AN |
| 3 | 90 | 0.43 | 0.79 | 18 | empty |
| 4 | 102 | 0.36 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–C · 3110 Ų buried · 66 hydrogen bonds · protein-protein
- B–D · 3072 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 613 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NVC · Crystal structure of TNKS2 in complex with 2-(3-hydroxyphenyl)-3,4-dihydroquinazolin-4-one · 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 5NVC · PDBe 5NVC · UniProt Q9H2K2
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