SMTL ID : 4n9c.1

Fragment-based Design of 3-Aminopyridine-derived Amides as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x 2ZM: 5-nitro-1H-benzimidazole(Non-covalent)

2ZM.1: 11 residues within 4Å: Chain A: H.191, F.193, D.219, S.241, V.242, A.244, S.275, I.309, R.311, I.351 Chain B: Y.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.193, A:F.193, A:V.242 Water bridges: A:A.245, A:R.311 2ZM.3: 11 residues within 4Å: Chain A: Y.18 Chain B: H.191, F.193, D.219, S.241, V.242, A.244, S.275, I.309, R.311, I.351 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Water bridges: A:Y.18 Hydrophobic interactions: B:F.193, B:F.193, B:V.242, B:A.244 Hydrogen bonds: B:S.275

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: R.40, R.392, S.398, K.400 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398, A:S.398 Water bridges: A:R.40, A:R.392, A:R.392, A:R.392, A:F.399, A:K.415, A:K.423, B:D.354 Salt bridges: A:R.40, A:R.392, A:K.400 PO4.4: 4 residues within 4Å: Chain B: R.40, R.392, S.398, K.400 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.398, B:S.398, B:K.415, B:K.415 Water bridges: B:R.40, B:R.40, B:R.392, B:R.392, B:R.392, B:F.399, B:K.400, B:K.400, B:K.423, B:K.423, B:K.423, A:R.196, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dragovich, P.S. et al., Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-02-19

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

Related Entries With Identical Sequence