SMTL ID : 5wi1.3 (2 other biounits)

Crystal structure of human NAMPT with fragment 5: (3E)-3-[(phenylamino)methylidene]oxan-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x AOY: (3E)-3-[(phenylamino)methylidene]oxan-2-one(Non-covalent)

AOY.1: 12 residues within 4Å: Chain A: H.191, F.193, R.196, D.219, S.241, V.242, A.244, S.275, R.311, I.351 Chain B: D.16, Y.18 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.193, A:D.219, A:V.242, A:A.244, B:D.16 Hydrogen bonds: A:D.219, A:S.275 Water bridges: A:R.311 Salt bridges: A:R.311 pi-Stacking: A:F.193, B:Y.18 AOY.3: 11 residues within 4Å: Chain A: D.16, Y.18 Chain B: H.191, F.193, R.196, D.219, S.241, V.242, A.244, S.275, R.311 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.193, B:F.193, B:D.219, B:V.242, B:A.244 Hydrogen bonds: B:D.219, B:S.275 Water bridges: B:R.311 Salt bridges: B:R.311 pi-Stacking: B:F.193, A:Y.18

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.40, R.392, S.398, K.400 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.398, A:S.398 Water bridges: A:R.40, A:R.392, A:R.392, A:F.399, A:K.400, A:K.415, A:K.415, A:K.423, A:K.423 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415, A:K.423 SO4.4: 5 residues within 4Å: Chain B: R.40, R.392, S.398, K.400, K.415 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.398 Water bridges: B:R.40, B:R.392, B:F.399, B:K.400, B:K.400, B:K.400, B:K.400, B:K.415, B:K.423, B:K.423 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415, B:K.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korepanova, A. et al., Fragment-based discovery of a potent NAMPT inhibitor. Bioorg. Med. Chem. Lett. (2018)

Release Date

2018-01-10

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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