SMTL ID : 5kit.1

Crystal Structure of Nicotinamide Phosphoribosyltransferase (Nampt) in Complex with Inhibitors 37

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x 6TA: ~{tert}-butyl (2~{S})-2-[(1,3-dihydropyrrolo[3,4-c]pyridin-2-ylcarbonylamino)methyl]-6-azaspiro[2.5]octane-6-carboxylate(Non-covalent)

6TA.1: 16 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, V.242, A.244, P.273, S.275, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 Ligands: PO4.3 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.191, A:D.219, A:V.242, A:P.273 Hydrogen bonds: A:S.275 Water bridges: A:D.219, A:D.219, A:A.245 pi-Stacking: A:F.193, B:Y.18 6TA.9: 15 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, P.273, S.275, I.309, R.311, A.379 Ligands: EDO.12 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.191, B:D.219, B:V.242, B:P.273 Hydrogen bonds: B:S.275 Water bridges: B:D.219, B:D.219, B:A.245 pi-Stacking: B:F.193, A:Y.18

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

PO4.2: 6 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: EDO.4, PO4.10 8 PLIP interactions: 7 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 Salt bridges: A:R.392, A:K.400 PO4.3: 8 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: 6TA.1, PO4.11 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 PO4.8: 6 residues within 4Å: Chain A: G.353, D.354, G.355, S.382, G.383, G.384 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 PO4.10: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: PO4.2 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Water bridges: A:Y.18, A:K.400, A:K.400, A:K.400, 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 PO4.11: 6 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: PO4.3, EDO.13 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Water bridges: B:E.149, B:F.399, B:K.400, B:K.415, B:K.415, B:K.415, B:K.423 Salt bridges: B:R.392, B:K.400 Hydrogen bonds: A:R.196 PO4.16: 7 residues within 4Å: Chain B: G.353, D.354, G.355, S.382, G.383, G.384 Ligands: EDO.12 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.353, B:G.355, B:G.383, B:G.384 Water bridges: B:D.354, B:D.354, B:V.356, B:V.356, A:R.392, A:R.392, A:D.393, A:D.393

9 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: PO4.2 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.5: 4 residues within 4Å: Chain A: G.315, P.317, D.354, G.355 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.315, A:D.354, A:G.355 EDO.6: 6 residues within 4Å: Chain A: 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.169 EDO.7: 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.12: 5 residues within 4Å: Chain A: R.392 Chain B: F.193, R.196 Ligands: 6TA.9, PO4.16 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:F.193, B:G.384, A:R.392 Hydrogen bonds: A:R.392 EDO.13: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.11 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, B:S.398 EDO.14: 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 EDO.15: 2 residues within 4Å: Chain B: K.323, E.326 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.322 EDO.17: 4 residues within 4Å: Chain B: G.315, P.317, D.354, G.355 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.315, B:D.354, B:G.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zak, M. et al., Minimizing CYP2C9 Inhibition of Exposed-Pyridine NAMPT (Nicotinamide Phosphoribosyltransferase) Inhibitors. J.Med.Chem. (2016)

Release Date

2016-08-31

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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