SMTL ID : 4lvb.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 1.84 Å

Oligo State

homo-dimer

Ligands

2 x 20N: N-[4-(acetylamino)phenyl]cyclopropanecarboxamide(Non-covalent)

20N.1: 11 residues within 4Å: Chain A: H.191, F.193, V.242, A.244, A.245, S.275, I.309, R.311, I.351, A.379 Chain B: Y.18 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.193, A:V.242, A:A.244, A:I.309, A:I.351, A:A.379, B:Y.18, B:Y.18 Hydrogen bonds: A:S.275 Water bridges: A:Y.188, A:H.191, A:D.219, A:V.242, A:R.311 20N.4: 12 residues within 4Å: Chain A: Y.18 Chain B: Y.188, H.191, F.193, V.242, A.244, A.245, S.275, I.309, R.311, I.351, A.379 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:F.193, B:V.242, B:A.244, B:I.309, B:I.351, B:A.379, A:Y.18, A:Y.18 Hydrogen bonds: B:S.275 Water bridges: B:Y.188, B:H.191, B:D.219, B:V.242 pi-Stacking: B:H.191

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

PO4.2: 6 residues within 4Å: Chain A: R.392, C.397, S.398, K.400, K.415 Chain B: R.196 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.40, A:S.398, B:R.196 Water bridges: A:R.392, A:D.393, A:D.393, A:F.399, A:K.400, A:K.415, A:K.415, A:K.423 Salt bridges: A:R.392, A:K.400, A:K.415 PO4.5: 5 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400, K.415 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.398, A:R.196 Water bridges: B:R.392, B:R.392, B:F.399, B:K.400, B:K.415, A:D.313, A:D.313 Salt bridges: B:R.392, B:K.400, B:K.415

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

EDO.3: 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:V.124, A:R.434, A:N.479 Water bridges: A:R.434 EDO.6: 3 residues within 4Å: Chain A: R.392 Chain B: G.383, G.384 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.392, B:G.383 Water bridges: B:V.356, B:G.384 EDO.7: 4 residues within 4Å: Chain A: G.197, G.383, G.384 Chain B: R.392 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.383, A:G.384, B:R.392 Water bridges: A:G.197, A:G.385, B: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
A

B
B

Nicotinamide phosphoribosyltransferase

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