SMTL ID : 4lts.1

Discovery of Potent and Efficacious Cyanoguanidine-containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x LTS: 2-cyano-1-pyridin-4-yl-3-(4-{[3-(trifluoromethoxy)phenyl]sulfonyl}benzyl)guanidine(Non-covalent)

LTS.1: 18 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, K.216, G.217, 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 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.191, A:V.242, A:V.242, A:I.309, A:I.351, B:Y.18, B:Y.18 Hydrogen bonds: A:D.219, A:D.219, A:S.241, A:S.275 Water bridges: A:R.311 pi-Stacking: A:H.191, A:F.193 Halogen bonds: A:K.216 LTS.7: 17 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, G.217, D.219, Y.240, S.241, V.242, A.244, S.275, I.309, R.311, I.351, A.379 13 PLIP interactions: 2 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:Y.18, A:Y.18, B:V.242, B:V.242, B:I.309, B:I.351 Hydrogen bonds: B:D.219, B:D.219, B:S.241, B:S.275 Water bridges: B:R.311 pi-Stacking: B:H.191, B:F.193

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

PO4.2: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.423 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398 Water bridges: A:R.40, A:R.40, A:R.392, A:R.392, A:R.392, A:K.400, A:K.400, A:K.415, A:K.423, B:R.196 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.8: 6 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, K.400, K.423 16 PLIP interactions: 1 interactions with chain A, 15 interactions with chain B Water bridges: A:R.196, B:R.40, B:R.392, B:R.392, B:R.392, B:N.396, B:K.400, B:K.415, B:K.415, B:K.415 Hydrogen bonds: B:S.398 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415, B:K.423

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

EDO.3: 6 residues within 4Å: Chain A: K.169, E.187, V.213, N.214, K.216, R.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.169, A:V.213 EDO.4: 5 residues within 4Å: Chain A: F.123, V.124, R.434, F.440, N.479 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.124, A:R.434, A:R.434, A:N.479 EDO.5: 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.6: 5 residues within 4Å: Chain A: G.353, G.355, G.383, G.384 Chain B: R.392 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.355, A:G.383, B:R.392 Water bridges: A:R.196, A:G.353, A:V.356, A:V.356, A:G.384, B:R.392 EDO.9: 7 residues within 4Å: Chain B: K.169, E.187, V.213, N.214, F.215, K.216, R.477 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.213 Water bridges: B:K.169 EDO.10: 6 residues within 4Å: Chain B: S.31, K.32, N.136, T.137, D.138, P.139 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.32, B:K.32, B:N.136 Water bridges: B:S.31 EDO.11: 4 residues within 4Å: Chain B: K.174, Y.175, E.178, K.369 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.174, B:K.369 Water bridges: B:K.369 EDO.12: 3 residues within 4Å: Chain A: R.392 Chain B: G.383, G.384 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.383, A:R.392 Water bridges: B:G.353, B:G.355, B:V.356, B:G.384, A:R.392 EDO.13: 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: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.251, A:C.401 Water bridges: B:E.246, B:S.248, A:N.146, A:F.399, A:C.401, A:V.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Discovery of potent and efficacious cyanoguanidine-containing nicotinamide phosphoribosyltransferase (Nampt) inhibitors. Bioorg.Med.Chem.Lett. (2014)

Release Date

2013-12-25

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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