SMTL ID : 7q8t.1

Crystal structure of NAMPT bound to ligand TSY535(compound 9a)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x 9IY: [(2~{R},3~{S},4~{R},5~{S})-3,4-bis(oxidanyl)-5-[4-[[[4-(phenylsulfonyl)phenyl]carbamoylamino]methyl]phenyl]oxolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

9IY.1: 19 residues within 4Å: Chain A: Y.194, H.197, F.199, R.202, Y.246, V.248, A.250, A.251, S.281, I.315, R.317, D.319, I.357, G.359, S.385 Chain B: Y.24, R.398, K.406 Ligands: SO4.4 30 PLIP interactions: 6 interactions with chain B, 24 interactions with chain A Hydrogen bonds: B:E.155, B:R.398, A:S.281, A:R.317 Water bridges: B:F.405, B:K.421, A:H.197, A:F.199, A:R.202, A:R.202, A:R.202, A:R.202, A:D.225, A:A.251, A:H.253, A:G.390 Salt bridges: B:R.398, B:K.406, A:R.202 Hydrophobic interactions: A:F.199, A:F.199, A:Y.246, A:V.248, A:V.248, A:I.315, A:I.315, A:I.357, A:I.357 pi-Stacking: A:H.197 pi-Cation interactions: A:R.317 9IY.3: 20 residues within 4Å: Chain A: Y.24, E.155, R.398, K.406 Chain B: Y.194, H.197, F.199, R.202, Y.246, V.248, A.250, A.251, S.281, I.315, R.317, D.319, I.357, G.359, S.385 Ligands: SO4.2 27 PLIP interactions: 22 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.199, B:F.199, B:Y.246, B:V.248, B:V.248, B:I.315, B:I.357 Hydrogen bonds: B:S.281, B:R.317, A:R.398 Water bridges: B:F.199, B:R.202, B:R.202, B:R.202, B:R.202, B:R.202, B:D.225, B:V.248, B:A.251, B:D.360, B:G.390, A:K.406, A:K.429 Salt bridges: B:R.202, A:R.398, A:K.406 pi-Cation interactions: B:R.317

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: R.398 Chain B: G.203, G.389, G.390, A.391 Ligands: 9IY.3 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:R.398, A:R.398, B:G.203, B:G.389 Salt bridges: A:R.398 Hydrogen bonds: B:G.390, B:A.391 SO4.4: 4 residues within 4Å: Chain A: G.203, G.390 Chain B: R.398 Ligands: 9IY.1 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.390 Water bridges: A:G.203, A:A.391, B:R.398, B:R.398, B:R.398 Salt bridges: B:R.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, S. et al., Chemistry-led investigations into the mode of action of NAMPT activators, resulting in the discovery of non-pyridyl class NAMPT activators. Acta Pharm Sin B (2023)

Release Date

2021-11-24

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase