SMTL ID : 4lvd.1

Fragment-based Identification of Amides Derived From trans-2-(Pyridin-3-yl)cyclopropanecarboxylic Acid as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.423 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.398, A:S.398 Water bridges: A:R.392, A:R.392, A:R.392, A:D.393, A:D.393, A:N.396, A:K.400, A:K.415, A:K.423 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415, A:K.423 PO4.2: 7 residues within 4Å: Chain A: G.353, G.355, V.356, S.382, G.383, G.384, G.385 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.355, A:V.356, A:G.383, A:G.384, A:G.385 Water bridges: A:G.353, A:V.356, B:R.392, B:R.392 PO4.5: 6 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, K.400, K.423 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.398, B:S.398 Water bridges: B:R.392, B:R.392, B:N.396, B:K.400, B:K.415, A:D.313, A:D.354, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415, B:K.423 PO4.6: 7 residues within 4Å: Chain A: R.392 Chain B: G.353, G.355, G.383, G.384, G.385 Ligands: EDO.4 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.355, B:G.383, B:G.384, B:G.385, A:R.392 Water bridges: B:D.354, B:V.356, B:V.356, B:V.356

2 x 1EB: N-(4-nitrophenyl)cyclopropanecarboxamide(Non-covalent)

1EB.3: 9 residues within 4Å: Chain A: H.191, F.193, R.196, D.219, S.241, V.242, A.244, R.311 Chain B: Y.18 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.18, A:F.193, A:V.242, A:A.244 pi-Stacking: B:Y.18, A:F.193 Hydrogen bonds: A:D.219 1EB.7: 10 residues within 4Å: Chain A: Y.18 Chain B: H.191, F.193, R.196, D.219, S.241, V.242, A.244, R.311 Ligands: EDO.4 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:F.193, B:V.242, B:A.244, A:Y.18 Hydrogen bonds: B:D.219 Water bridges: B:D.313, B:D.313, B:G.353 pi-Stacking: B:F.193, A:Y.18

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

EDO.4: 6 residues within 4Å: Chain A: R.392 Chain B: R.196, G.197, G.384 Ligands: PO4.6, 1EB.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.392, B:G.384 Water bridges: A:R.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Identification of amides derived from 1H-pyrazolo[3,4-b]pyridine-5-carboxylic acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-09-25

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Nicotinamide phosphoribosyltransferase

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