MolNFT v1 · #143222 · protein
Crystal structure of human nampt in complex with nvp-LOD812
6ATB · Nicotinamide phosphoribosyltransferase: “Crystal structure of human nampt in complex with nvp-LOD812”. X-ray diffraction, 2 ligands (BWA, PO4), 15 pockets (best druggability 0.80). MolNFT v1 #143222 on GenesisL1: 3D structure…
- PDB
- 6ATB
- Type
- protein
- Length
- 1,870 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
- BWA, PO4
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 466 | 40% helix, 19% strand | P43490 |
| B | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 470 | 42% helix, 19% strand | P43490 |
| D | Nicotinamide phosphoribosyltransferase (EC 2.4.2.12) | protein | 468 | 40% helix, 19% strand | P43490 |
Ligands and binding sites
- BWA · N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl) methyl]phenyl}-N'-[(pyridin-3-yl)methyl]urea · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.80 | 0.83 | 87 | BWA, PO4 |
| 2 | 765 | 0.80 | 0.84 | 82 | BWA, PO4 |
| 3 | 800 | 0.80 | 0.83 | 80 | PO4, BWA |
| 4 | 755 | 0.79 | 0.83 | 81 | PO4, BWA |
| 5 | 613 | 0.71 | 0.79 | 63 | DMS, GOL |
Interfaces
5 interfaces between chains.
- C–D · 4354 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 4264 Ų buried · 74 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 65 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ATB · Crystal Structure of human NAMPT in complex with NVP-LOD812 · 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 6ATB · PDBe 6ATB · UniProt P43490
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