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Crystal structure of human nampt with fragment 2: 2-[(2-fluorophenyl) amino]-6-propylpyrimidin-4(3H)-one

Analyse Crystal structure of human nampt with fragment 2: 2-[(2-fluorophenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WI0
Type: protein
Length: 928 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: AQ1
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nicotinamide phosphoribosyltransferase (EC 2.4.2.12)	protein	464	41% helix, 19% strand	P43490

Ligands and binding sites

AQ1 · 2-[(2-fluorophenyl)amino]-6-propylpyrimidin-4(3H)-one · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	668	0.79	0.84	78	AQ1
2	726	0.79	0.83	87	AQ1
3	563	0.70	0.79	47	empty
4	74	0.34	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 4310 Å² buried · 81 hydrogen bonds · protein-protein

Compared structures

5WI0 · Crystal structure of human NAMPT with fragment 2… · 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 5WI0 · PDBe 5WI0 · UniProt P43490

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