MolNFT v1 · #100884 · protein
Inhibitors of 4-phosphopanthetheine adenylyltransferase
4NAT · Phosphopantetheine adenylyltransferase: “Inhibitors of 4-phosphopanthetheine adenylyltransferase”. X-ray diffraction, 2 ligands (2W5, ADP), 4 pockets (best druggability 0.74). MolNFT v1 #100884 on GenesisL1: 3D structure, binding…
- PDB
- 4NAT
- Type
- protein
- Length
- 464 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- P63820
- Ligands
- 2W5, ADP
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 153 | 47% helix, 19% strand | P63820 |
| B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 156 | 44% helix, 20% strand | P63820 |
| C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 155 | 45% helix, 19% strand | P63820 |
Ligands and binding sites
- 2W5 · (1R,2R)-N-(3,4-dichlorobenzyl)-2-(4,6-dimethoxypyrimidin-2-yl)cyclohexanecarboxamide · ligand · 3 copies · chains A, B, C
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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 | 506 | 0.74 | 0.82 | 50 | 2W5, ADP |
| 2 | 514 | 0.73 | 0.82 | 50 | 2W5, ADP |
| 3 | 475 | 0.73 | 0.82 | 53 | 2W5, ADP |
| 4 | 68 | 0.34 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 567 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 559 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4NAT · Inhibitors of 4-Phosphopanthetheine Adenylyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- P63820 · AlphaFold monomer V2.0 prediction for phosphopantetheine adenylyltransferase (P63820) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P63820
- Elsewhere: RCSB PDB 4NAT · PDBe 4NAT · UniProt P63820
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