SMTL ID : 4kfn.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x 1QR: N-[4-(piperidin-1-ylsulfonyl)benzyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxamide(Non-covalent)

1QR.1: 15 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, S.275, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.188, A:F.193, A:V.242, B:Y.18 Hydrogen bonds: A:D.219, A:D.219, A:S.241, A:S.275 pi-Stacking: A:H.191, A:F.193, A:F.193, B:Y.18 1QR.10: 15 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, S.275, I.309, R.311, I.351, A.379 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:V.242, A:Y.18 Hydrogen bonds: B:D.219, B:D.219, B:S.241, B:S.275 Water bridges: B:H.191, B:R.311 pi-Stacking: B:H.191, B:F.193, B:F.193, A:Y.18

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

PO4.2: 6 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:Y.18, A:H.247, A:D.313 Water bridges: B:K.400, A:R.196, A:R.196, A:R.196, A:H.247, A:S.248 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.4, PO4.12 10 PLIP interactions: 8 interactions with chain A, 2 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, B:R.196 Salt bridges: A:R.392, A:K.400 PO4.5: 3 residues within 4Å: Chain A: G.383, G.384 Chain B: R.392 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Water bridges: B:R.392, B:R.392, B:R.392, B:D.393, A:G.355, A:V.356, A:G.384, A:G.385 Salt bridges: B:R.392 Hydrogen bonds: A:G.383, A:G.384 PO4.11: 5 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: EDO.13 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:R.196 Water bridges: A:D.313, A:D.354, B:E.149, 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.423 Salt bridges: B:R.392, B:K.400 PO4.12: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: PO4.3 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Water bridges: A:K.400, A:K.400, B:R.196, B:R.196, B:R.196, B:S.248, B:D.313 Hydrogen bonds: B:H.247 Salt bridges: B:R.196, B:H.247, B:R.311 PO4.14: 3 residues within 4Å: Chain A: R.392 Chain B: G.383, G.384 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.383, B:G.384, A:R.392 Water bridges: B:G.353, B:G.381, B:S.382, B:G.385, A:D.393, A:D.393

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

EDO.4: 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:R.392, A:D.393, A:D.393, A:N.396, A:S.398 EDO.6: 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:R.434, A:N.479 EDO.7: 4 residues within 4Å: Chain A: N.67, K.71, K.229, Y.230 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.71 Water bridges: A:N.67, A:Y.230, A:Y.230 EDO.8: 6 residues within 4Å: Chain A: S.31, K.32, N.136, T.137, D.138, P.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.32, A:N.136 EDO.9: 5 residues within 4Å: Chain A: P.27, P.28, N.29, T.406, N.407 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.407 EDO.13: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:R.392, B:D.393, B:D.393, B:N.396, B:S.398 EDO.15: 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.16: 6 residues within 4Å: Chain B: S.31, K.32, N.136, T.137, D.138, P.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.32, B:K.32 EDO.17: 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:K.169, B:V.213 EDO.18: 4 residues within 4Å: Chain B: F.123, V.124, F.440, N.479 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.124, B:V.124, B:N.479 Water bridges: B:R.434

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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