SMTL ID : 4jr5.1

Structure-based Identification of Ureas as Novel Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x 1LS: 1-[4-(piperidin-1-ylsulfonyl)phenyl]-3-(pyridin-3-ylmethyl)thiourea(Non-covalent)

1LS.1: 13 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, V.242, A.244, S.275, I.309, R.311, I.351, A.379 Chain B: Y.18 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.219, A:V.242, A:I.351 Water bridges: A:D.219, A:D.219, A:R.311 pi-Stacking: A:H.191, A:F.193, B:Y.18 1LS.5: 13 residues within 4Å: Chain A: Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, V.242, A.244, S.275, I.309, R.311, I.351, A.379 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B pi-Stacking: A:Y.18, B:H.191, B:F.193 Hydrophobic interactions: B:D.219, B:V.242, B:I.351 Water bridges: B:V.242, B:V.242

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

PO4.2: 5 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.398, A:S.398 Water bridges: A:R.40, A:R.392, A:N.396, A:K.400, A:K.400, A:K.415, A:K.423 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.3: 6 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.247, B:Y.18 Water bridges: A:R.196, A:R.196, A:R.196, A:H.247, A:S.248, A:R.311, A:R.311, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.6: 6 residues within 4Å: Chain A: R.196 Chain B: R.40, R.392, C.397, S.398, K.400 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.398, B:K.415, A:R.196 Water bridges: B:R.40, B:R.40, B:F.399, B:K.400, B:K.423, A:D.313, A:D.354, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400 PO4.7: 5 residues within 4Å: Chain B: G.353, G.355, S.382, G.383, G.384 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Water bridges: A:R.392, A:R.392, A:R.392, B:V.356, B:V.356, B:G.385 Hydrogen bonds: B:G.355, B:G.383, B:G.384

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: F.123, V.124, R.434, F.440, N.479 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.122, A:V.124, A:R.434 Water bridges: A:R.434 EDO.8: 4 residues within 4Å: Chain A: Y.18 Chain B: E.246, H.247, R.311 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Water bridges: A:Y.18, A:E.149, A:K.400, B:R.196, B:R.196 Hydrogen bonds: B:H.247, B:R.311, B:R.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Structure-based identification of ureas as novel nicotinamide phosphoribosyltransferase (nampt) inhibitors. J.Med.Chem. (2013)

Release Date

2013-05-08

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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