SMTL ID : 4kfo.1

Structure-Based Discovery of Novel Amide-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x 1QS: N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}imidazo[1,2-a]pyridine-6-carboxamide(Non-covalent)

1QS.1: 18 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, P.273, S.275, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 Ligands: PO4.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.191, A:V.242, A:V.242, A:I.309, A:I.351 Hydrogen bonds: A:D.219 Water bridges: A:R.311 pi-Stacking: A:H.191, A:F.193, A:F.193, B:Y.18 Halogen bonds: A:Y.240 1QS.11: 18 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, P.273, S.275, I.309, R.311, I.351, A.379 Ligands: PO4.13 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.242, B:V.242, B:I.309, B:I.351 Hydrogen bonds: B:D.219 Water bridges: B:R.311 pi-Stacking: B:H.191, B:F.193, B:F.193, A:Y.18 Halogen bonds: B:Y.240

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

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

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

EDO.4: 4 residues within 4Å: Chain A: G.315, P.317, D.354, G.355 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.315, A:D.354, A:G.355, A:G.355, A:G.355 EDO.5: 4 residues within 4Å: Chain A: G.353, G.355, G.383, G.384 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.353, A:G.383, A:G.384 Water bridges: A:G.385, B:R.392, B:R.392, B:R.392 EDO.6: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:R.392, A:N.396, A:S.398 EDO.7: 6 residues within 4Å: Chain A: S.31, K.32, N.136, T.137, D.138, P.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.32, A:T.137 Water bridges: A:S.31 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 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.9: 7 residues within 4Å: Chain A: K.169, E.187, V.213, N.214, F.215, K.216, R.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.169, A:V.213 EDO.10: 4 residues within 4Å: Chain A: 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.14: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:R.392, B:N.396, B:S.398 Water bridges: B:K.423 EDO.15: 3 residues within 4Å: Chain B: G.353, G.383, G.384 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.353, B:G.383, B:G.384 Water bridges: B:G.355, B:G.385, A:R.392, A:R.392 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 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:E.246, A:E.246, A:S.248, B:N.146, B:C.401, B:V.413 Hydrogen bonds: B:C.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Structure-based identification of ureas as novel nicotinamide phosphoribosyltransferase (nampt) inhibitors. J.Med.Chem. (2013)

Release Date

2013-05-08

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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