MolNFT v1 · #38383 · protein
Crystal structure of human nmprtase in complex with FK866
2GVJ · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nmprtase in complex with FK866”. X-ray diffraction, 1 ligand (DGB), 8 pockets (best druggability 0.80). MolNFT v1 #38383 on GenesisL1: 3D structure, binding sites…
- PDB
- 2GVJ
- Type
- protein
- Length
- 929 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- P43490
- Ligands
- DGB
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 465 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 464 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- DGB · (2E)-N-{4-[1-(benzenecarbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.80 | 0.84 | 78 | DGB |
| 2 | 749 | 0.79 | 0.83 | 86 | DGB |
| 3 | 531 | 0.69 | 0.78 | 49 | empty |
| 4 | 50 | 0.32 | 0.78 | 16 | empty |
| 5 | 67 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4319 Ų buried · 78 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2GVJ · Crystal Structure of Human NMPRTase in complex with FK866 · 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 P43490
- Elsewhere: RCSB PDB 2GVJ · PDBe 2GVJ · UniProt P43490
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