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: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.240, B:V.242, B:P.273, A:Q.92 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

Yu, S.S. et al., NAMPT, an antiglioma target of the phenanthroindolizidine alkaloid PF403, was identified by cellular thermal proteome profiling (TPP). To Be Published

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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