MolNFT v1 · #143696 · protein
Crystal structure of human nampt in complex with nvp-LVR596
6B76 · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nampt in complex with nvp-LVR596”. X-ray diffraction, 2 ligands (CVJ, PO4), 13 pockets (best druggability 0.80). MolNFT v1 #143696 on GenesisL1: 3D structure…
- PDB
- 6B76
- Type
- protein
- Length
- 1,878 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
- CVJ, PO4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 470 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 468 | 41% helix, 19% strand | P43490 |
| C | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 469 | 41% helix, 19% strand | P43490 |
| D | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 471 | 40% helix, 19% strand | P43490 |
Ligands and binding sites
- CVJ · (1S,2S)-N-{4-[(1S)-1-(propanoylamino)ethyl]phenyl}-2-(pyridin-3-yl)cyclopropane-1-carboxamide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.80 | 0.84 | 80 | PO4, CVJ |
| 2 | 775 | 0.80 | 0.83 | 86 | CVJ, PO4 |
| 3 | 1143 | 0.79 | 0.81 | 91 | empty |
| 4 | 737 | 0.79 | 0.83 | 79 | PO4, CVJ |
| 5 | 746 | 0.79 | 0.83 | 76 | CVJ, PO4 |
Interfaces
5 interfaces between chains.
- C–D · 4423 Ų buried · 86 hydrogen bonds · protein-protein
- A–B · 4417 Ų buried · 77 hydrogen bonds · protein-protein
- A–D · 169 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6B76 · Crystal Structure of human NAMPT in complex with NVP-LVR596 · 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 6B76 · PDBe 6B76 · UniProt P43490
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