MolNFT v1 · #143695 · protein
Crystal structure of human nampt in complex with nvp-LOQ594
6B75 · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nampt in complex with nvp-LOQ594”. X-ray diffraction, 1 ligand (CVP), 17 pockets (best druggability 0.81). MolNFT v1 #143695 on GenesisL1: 3D structure, binding…
- PDB
- 6B75
- Type
- protein
- Length
- 1,865 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide phosphoribosyltransferase
- EC
- 2.4.2.12
- UniProt
- P43490
- Ligands
- CVP
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 466 | 42% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 467 | 40% helix, 19% strand | P43490 |
Ligands and binding sites
- CVP · 4-[(piperazin-1-yl)methyl]-N-{[4-({[(pyridin-3-yl) methyl]carbamoyl}amino)phenyl]methyl}benzamide · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.81 | 0.84 | 78 | empty |
| 2 | 778 | 0.80 | 0.84 | 83 | CVP |
| 3 | 800 | 0.79 | 0.82 | 92 | CVP |
| 4 | 752 | 0.78 | 0.82 | 73 | CVP |
| 5 | 616 | 0.71 | 0.79 | 62 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4353 Ų buried · 77 hydrogen bonds · protein-protein
- A–B · 4272 Ų buried · 72 hydrogen bonds · protein-protein
- B–C · 121 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6B75 · Crystal Structure of human NAMPT in complex with NVP-LOQ594 · 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 6B75 · PDBe 6B75 · UniProt P43490
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