SMTL ID : 4lva.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 1.55 Å

Oligo State

homo-dimer

Ligands

2 x 20M: N-(4-{[4-(pyrrolidin-1-yl)piperidin-1-yl]sulfonyl}benzyl)-2H-pyrido[4,3-e][1,2,4]thiadiazin-3-amine 1,1-dioxide(Non-covalent)

20M.1: 16 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, A.245, S.275, I.309, R.311, I.351, A.379 Chain B: Y.18 Ligands: EDO.7 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.188, A:Y.188, A:Y.188, A:F.193, A:V.242, A:I.309 Hydrogen bonds: A:D.219, A:S.241, A:S.275, A:R.311 Water bridges: A:A.245 pi-Stacking: A:H.191, A:F.193, B:Y.18 pi-Cation interactions: A:Y.188 20M.11: 15 residues within 4Å: Chain A: Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, A.245, 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:Y.188, B:V.242, B:I.309, B:I.351 Hydrogen bonds: B:D.219, B:S.241, B:S.275, B:R.311 Water bridges: B:H.191, B:A.245 pi-Stacking: B:H.191, B:F.193, A:Y.18 pi-Cation interactions: B:Y.188

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

PO4.2: 7 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: PO4.12 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.247, A:D.313, B:Y.18 Water bridges: A:R.196, A:R.196, A:R.196, A:H.247, A:S.248, A:R.311, B:E.149, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.3: 6 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: EDO.6, PO4.13 12 PLIP interactions: 11 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:F.399, A:K.400, A:K.415, A:K.423, A:K.423 Salt bridges: A:R.392, A:K.400 PO4.4: 8 residues within 4Å: Chain A: F.193, G.194, R.196, G.197, G.383, G.384 Chain B: R.392 Ligands: EDO.10 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:F.193, A:G.197, A:G.384 Water bridges: A:F.193, A:G.385, B:R.392, B:R.392, B:R.392, B:R.392 Salt bridges: B:R.392 PO4.12: 6 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: PO4.2, EDO.15 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Water bridges: B:E.149, B:R.392, B:R.392, B:R.392, B:F.399, B:F.399, B:K.400, B:K.400, B:K.415, B:K.415, B:K.415, B:K.423, B:K.423, A:D.313, A:D.354 Salt bridges: B:R.392, B:K.400 Hydrogen bonds: A:R.196 PO4.13: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: PO4.3 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:Y.18, B:H.247 Water bridges: A:K.400, A:K.400, A:K.400, B:R.196, B:R.196, B:R.196, B:R.196, B:S.248, B:R.311 Salt bridges: B:R.196, B:H.247, B:R.311 PO4.14: 8 residues within 4Å: Chain A: R.392 Chain B: F.193, G.194, R.196, G.197, G.383, G.384 Ligands: EDO.18 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.197, B:G.384 Water bridges: B:G.385, A:R.392, A:R.392, A:R.392, A:R.392 Salt bridges: A:R.392

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

EDO.5: 7 residues within 4Å: Chain A: K.169, E.187, V.213, N.214, F.215, K.216, R.477 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.187, A:E.187, A:V.213 Water bridges: A:K.216 EDO.6: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:D.393, A:D.393, A:N.396, A:S.398, A:S.398 EDO.7: 7 residues within 4Å: Chain A: K.189, I.309, R.349, V.350, I.378, A.379 Ligands: 20M.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.189, A:K.189, A:V.350, A:A.379 EDO.8: 5 residues within 4Å: Chain A: G.315, P.317, D.354, G.355 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.355 EDO.9: 6 residues within 4Å: Chain A: G.122, F.123, V.124, R.434, F.440, N.479 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.122, A:V.124, A:R.434 EDO.10: 5 residues within 4Å: Chain A: G.353, D.354, G.355, G.384 Ligands: PO4.4 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Water bridges: B:R.392, B:R.392, B:R.392, B:R.392, B:D.393, B:D.393, A:V.356, A:G.385 Hydrogen bonds: A:D.354, A:D.354, A:G.355, A:G.384 EDO.15: 8 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.12, EDO.17 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:D.393, B:D.393, B:N.396, B:S.398, B:S.398 EDO.16: 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: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:E.246, A:S.248, B:N.146, B:C.401, B:V.413 Hydrogen bonds: B:C.401 EDO.17: 6 residues within 4Å: Chain B: R.40, D.393, N.396, K.423 Ligands: EDO.8, EDO.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.40, B:K.423, B:K.423 Water bridges: B:N.396 EDO.18: 5 residues within 4Å: Chain B: G.353, D.354, G.355, G.384 Ligands: PO4.14 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Water bridges: A:R.392, A:R.392, A:R.392, A:D.393, B:V.356, B:G.385 Hydrogen bonds: B:D.354, B:G.355, B:G.384 EDO.19: 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: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.251, A:C.401 Water bridges: B:E.246, B:E.246, B:S.248, A:N.146, A:C.401, A:V.413 EDO.20: 6 residues within 4Å: Chain A: Y.195, A.222 Chain B: F.9, N.10, L.13, A.14 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.8, B:N.10, B:L.13, A:Y.195

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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