SMTL ID : 4lvf.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 1.50 Å

Oligo State

homo-dimer

Ligands

2 x 20P: (1S,2S)-2-phenyl-N-(pyridin-4-yl)cyclopropanecarboxamide(Non-covalent)

20P.1: 13 residues within 4Å: Chain A: H.191, F.193, R.196, D.219, V.242, A.244, A.245, S.275, I.309, R.311, I.351 Chain B: D.16, Y.18 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.193, A:F.193, A:D.219, A:V.242, A:A.244, A:I.351, B:Y.18 Hydrogen bonds: A:S.275 Water bridges: A:D.219, A:D.219 pi-Stacking: A:F.193, B:Y.18 20P.11: 13 residues within 4Å: Chain A: D.16, Y.18 Chain B: H.191, F.193, R.196, D.219, V.242, A.244, A.245, S.275, I.309, R.311, I.351 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:F.193, B:D.219, B:V.242, B:A.244, B:I.351, A:Y.18 Hydrogen bonds: B:S.275 Water bridges: B:D.219, B:S.241 pi-Stacking: B:F.193, A:Y.18

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

PO4.2: 5 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: EDO.3 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398, B:R.196 Water bridges: A:R.392, A:R.392, A:R.392, A:F.399, A:K.400, A:K.415 Salt bridges: A:R.392, A:K.400 PO4.12: 5 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: EDO.15 16 PLIP interactions: 5 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.196 Water bridges: A:D.313, A:D.313, A:D.354, A:D.354, B:E.149, B:R.392, B:R.392, B:F.399, B:F.399, B:K.400, B:K.400, B:K.415, B:K.423 Salt bridges: B:R.392, B:K.400

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

EDO.3: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.2 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: G.315, P.317, D.354, G.355 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: G.353, G.383, G.384 Chain B: R.392 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: K.228, T.233, K.234, D.235, P.236 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: F.123, V.124, R.434, F.440, N.479 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: K.400, C.401, F.414, K.415, S.425 Chain B: H.247, S.248, T.251 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: R.196, E.246, H.247, R.311 Chain B: Y.18, K.400 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: E.187, V.213, N.214, F.215, K.216, R.477 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: R.392 Chain B: G.353, G.383, G.384 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: G.315, P.317, D.354, G.355 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.12 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: N.67, K.71, K.229, Y.230 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: K.169, E.187, V.213, N.214, F.215, K.216, R.477 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain A: H.247, S.248, T.251 Chain B: K.400, C.401, F.414, K.415, S.425 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: G.122, F.123, V.124, F.440, N.479 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: Y.18, K.400 Chain B: E.246, H.247, R.311 Ligand excluded by PLIP

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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