SMTL ID : 4lvg.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

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 20O: (1S,2S)-N-[4-(phenylsulfonyl)phenyl]-2-(pyridin-3-yl)cyclopropanecarboxamide(Non-covalent)

20O.1: 16 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, V.242, A.244, A.245, P.273, S.275, I.309, R.311, I.351, A.379 Chain B: Y.18 Ligands: EDO.18 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.193, A:D.219, A:V.242, A:A.244, A:P.273, A:I.309, A:I.351, B:Y.18 Hydrogen bonds: A:S.275 Water bridges: A:D.219, A:V.242 pi-Stacking: A:H.191, A:F.193, B:Y.18 20O.12: 17 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, V.242, A.244, A.245, P.273, S.275, I.309, R.311, I.351, A.379 Ligands: EDO.11 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:D.219, B:V.242, B:V.242, B:A.244, B:P.273, B:I.309, B:I.351, A:Y.18 Hydrogen bonds: B:S.275 Water bridges: B:D.219, B:V.242 pi-Stacking: B:H.191, B:F.193, A:Y.18

6 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.5 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, B:R.196 Water bridges: A:R.392, A:F.399, A:K.400, A:K.415, A:K.415, A:K.423 Salt bridges: A:R.392, A:K.400 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:D.313, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.4: 7 residues within 4Å: Chain A: G.353, D.354, G.355, S.382, G.383, G.384 Ligands: EDO.18 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.353, A:D.354, A:G.355, A:V.356, A:G.383, A:G.384 Water bridges: A:V.356, A:V.356, A:G.385, B:R.392, B:R.392, B:R.392 PO4.13: 6 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Water bridges: A:K.400, A:K.400, A:K.400, B:R.196, B:R.196, B:R.196, B:S.248, B:R.311, B:R.311 Hydrogen bonds: B:H.247 Salt bridges: B:R.196, B:H.247, B:R.311 PO4.14: 6 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: EDO.16, EDO.18 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.398, A:R.196 Water bridges: B:E.149, B:F.399, B:K.400, B:K.415, B:K.415, B:K.415, B:K.415, A:D.313 Salt bridges: B:R.392, B:K.400 PO4.15: 7 residues within 4Å: Chain B: G.353, D.354, G.355, S.382, G.383, G.384 Ligands: EDO.11 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Water bridges: A:R.392, A:R.392, A:R.392, B:V.356, B:V.356, B:V.356, B:V.356 Hydrogen bonds: B:G.355, B:V.356, B:G.383, B:G.384

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

EDO.5: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:N.396, A:S.398, A:S.398 Water bridges: A:K.423 EDO.6: 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.7: 8 residues within 4Å: Chain A: H.247, S.248, T.251 Chain B: K.400, C.401, F.414, K.415, S.425 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.401 Water bridges: B:N.146, B:C.401, B:V.413, A:E.246, A:S.248 EDO.8: 7 residues within 4Å: Chain A: F.9, N.10, L.13, A.14 Chain B: Y.195, Q.201, A.222 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.195, A:N.10, A:N.10 EDO.9: 3 residues within 4Å: Chain A: G.315, D.354, G.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.315 EDO.10: 5 residues within 4Å: Chain A: E.187, V.213, N.214, K.216, R.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.213 Water bridges: A:K.169 EDO.11: 5 residues within 4Å: Chain A: R.392 Chain B: F.193, R.196 Ligands: 20O.12, PO4.15 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.392 Water bridges: A:R.392, B:R.311, B:R.311, B:R.311, B:G.384 EDO.16: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:N.396, B:S.398, B:S.398 Water bridges: B:K.423 EDO.17: 4 residues within 4Å: Chain B: G.315, P.317, D.354, G.355 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:G.315, B:G.355, A:D.420 EDO.18: 6 residues within 4Å: Chain A: F.193, R.196 Chain B: R.392 Ligands: 20O.1, PO4.4, PO4.14 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:R.311, A:R.311, A:R.311, A:G.384, B:R.392 Hydrogen bonds: 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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