SMTL ID : 4n9d.1

Fragment-based Design of 3-Aminopyridine-derived Amides as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 2HJ: 4-({[(4-tert-butylphenyl)sulfonyl]amino}methyl)-N-(pyridin-3-yl)benzamide(Non-covalent)

2HJ.1: 16 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, S.275, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.188, A:Y.188, A:F.193, A:F.193, A:D.219, A:Y.240, A:V.242, A:V.242, A:A.244, A:I.351 Hydrogen bonds: A:H.191, A:D.219, A:R.311 Water bridges: A:R.311 pi-Stacking: A:F.193, B:Y.18 2HJ.8: 16 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, S.275, I.309, R.311, I.351, A.379 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.188, B:Y.188, B:F.193, B:F.193, B:D.219, B:Y.240, B:V.242, B:V.242, B:A.244, B:I.351 Hydrogen bonds: B:H.191, B:D.219, B:R.311, B:R.311 pi-Stacking: B:F.193, A:Y.18

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

PO4.2: 4 residues within 4Å: Chain A: R.40, R.392, S.398, K.400 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.398, A:S.398, A:S.398, A:K.415 Water bridges: A:R.392, A:R.392, A:D.393, A:D.393, A:F.399, A:K.400, A:K.400 Salt bridges: A:R.40, A:R.392, A:K.400 PO4.9: 4 residues within 4Å: Chain B: R.40, R.392, S.398, K.400 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain B Water bridges: A:R.196, A:D.313, A:D.354, A:D.354, A:D.354, B:R.40, B:R.40, B:R.392, B:R.392, B:R.392, B:F.399, B:K.400, B:K.415 Hydrogen bonds: B:S.398, B:S.398 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415

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

EDO.3: 8 residues within 4Å: Chain A: K.400, C.401, F.414, K.415, S.425 Chain B: H.247, S.248, T.251 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.401, B:T.251 Water bridges: A:N.146, A:F.399, A:C.401, A:V.413, B:E.246, B:S.248 EDO.4: 6 residues within 4Å: Chain A: K.169, E.187, V.213, N.214, K.216, R.477 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.477 EDO.5: 5 residues within 4Å: Chain A: G.122, F.123, V.124, R.434, 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: 8 residues within 4Å: Chain A: H.247, S.248, T.251 Chain B: K.400, C.401, F.414, K.415, S.425 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:C.401 Water bridges: B:F.399, B:C.401, B:V.413, A:E.246, A:E.246, A:S.248 EDO.7: 5 residues within 4Å: Chain A: E.246, H.247, R.311 Chain B: Y.18, K.400 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Y.18, A:H.247, A:H.247, A:R.311, A:R.311 Water bridges: B:K.400, A:R.196, A:R.196, A:R.196 EDO.10: 5 residues within 4Å: Chain A: Y.18, K.400 Chain B: E.246, H.247, R.311 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Water bridges: A:Y.18, 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

Dragovich, P.S. et al., Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-02-19

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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