SMTL ID : 8y55.1

Crystal Structure of NAMPT-PF403

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x 01: (13~{a}~{S})-6,7-dimethoxy-9,11,12,13,13~{a},14-hexahydrophenanthro[9,10-f]indolizin-3-ol

01.1: 14 residues within 4Å: Chain A: Y.188, H.191, G.217, Y.240, S.241, V.242, P.273, T.304, Q.305, P.307, I.309 Chain B: Q.92 Ligands: PEG.2, PEG.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.240, A:V.242, A:P.273, B:Q.92 Hydrogen bonds: A:H.191 pi-Stacking: A:Y.188, A:Y.188 01.5: 11 residues within 4Å: Chain A: Q.92 Chain B: Y.188, H.191, Y.240, S.241, V.242, P.273, T.304, Q.305, P.307 Ligands: PEG.6 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.92, B:Y.240, B:V.242, B:P.273 Hydrogen bonds: B:H.191 pi-Stacking: B:Y.188

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: Y.188, D.235, Y.240 Chain B: Q.92 Ligands: 01.1, PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.188, A:D.235 PEG.3: 4 residues within 4Å: Chain A: G.185, Y.188 Ligands: 01.1, PEG.2 No protein-ligand interaction detected (PLIP) PEG.4: 5 residues within 4Å: Chain A: N.67, K.68, K.71, K.229, Y.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.71, A:K.229 PEG.6: 2 residues within 4Å: Chain B: Y.188 Ligands: 01.5 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, F. et al., Thermal proteome profiling (TPP) reveals NAMPT as the anti-glioma target of phenanthroindolizidine alkaloid PF403. Acta Pharm Sin B (2025)

Release Date

2025-02-19

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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