MolNFT v1 · #143433 · protein
Crystal structure of human nampt in complex with nvp-LQN520
6AZJ · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nampt in complex with nvp-LQN520”. X-ray diffraction, 1 ligand (C5V), 7 pockets (best druggability 0.80). MolNFT v1 #143433 on GenesisL1: 3D structure, binding…
- PDB
- 6AZJ
- 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
- C5V
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 467 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 462 | 40% helix, 19% strand | P43490 |
Ligands and binding sites
- C5V · (1S,2S)-N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl) methyl]phenyl}-2-(pyridin-3-yl)cyclopropane-1-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.80 | 0.82 | 111 | C5V |
| 2 | 996 | 0.80 | 0.81 | 84 | C5V |
| 3 | 514 | 0.70 | 0.79 | 54 | empty |
| 4 | 63 | 0.33 | 0.77 | 16 | empty |
| 5 | 61 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3833 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 6AZJ · Crystal Structure of human NAMPT in complex with NVP-LQN520 · 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 6AZJ · PDBe 6AZJ · UniProt P43490
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