Research workbench
Crystal structure of human nampt in complex with nvp-LTM976
Analyse Crystal structure of human nampt in complex with nvp-LTM976 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PEB
- Type
- protein
- Length
- 1,877 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
- OE4, PO4
- Pockets
- 16 · best druggability 0.81
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 | 469 | 41% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 468 | 40% helix, 19% strand | P43490 |
| C | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 469 | 40% helix, 19% strand | P43490 |
| D | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 471 | 41% helix, 19% strand | P43490 |
Ligands and binding sites
- OE4 · N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl) methyl]phenyl}-3-(pyridin-3-yl)azetidine-1-carboxamide · ligand · 3 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.81 | 0.82 | 82 | empty |
| 2 | 734 | 0.80 | 0.84 | 86 | PO4 |
| 3 | 696 | 0.79 | 0.84 | 80 | PO4, OE4 |
| 4 | 749 | 0.79 | 0.83 | 80 | OE4, PO4 |
| 5 | 753 | 0.79 | 0.83 | 80 | OE4, PO4 |
Interfaces
5 interfaces between chains.
- A–B · 4446 Ų buried · 76 hydrogen bonds · protein-protein
- C–D · 4353 Ų buried · 85 hydrogen bonds · protein-protein
- A–D · 195 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 115 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PEB · Crystal Structure of human NAMPT in complex with NVP-LTM976 · the same entry in another collection · chain B against B, 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 6PEB · PDBe 6PEB · UniProt P43490
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.