SMTL ID : 8ivu.1 (1 other biounit)

Crystal Structure of Human NAMPT in complex with A4276

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

2 x SJ6: N-[[4-(6-methyl-1,3-benzoxazol-2-yl)phenyl]methyl]pyridine-3-carboxamide(Non-covalent)

SJ6.1: 19 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, R.349, V.350, I.351, N.377, I.378, A.379 Chain B: D.16, Y.18 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.242, A:I.309, A:R.349, A:I.351, A:A.379 Hydrogen bonds: A:R.196, A:D.219 Water bridges: A:H.191, A:H.191, A:Y.195, A:R.311 pi-Stacking: A:H.191, A:F.193, B:Y.18 SJ6.5: 18 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, R.349, V.350, I.351, I.378, A.379 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:V.242, B:I.309, B:R.349, B:I.351, B:A.379, A:Y.18 Hydrogen bonds: B:R.196, B:D.219 Water bridges: B:Y.195, B:R.311, A:D.16 pi-Stacking: B:H.191, B:F.193

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: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.247, B:Y.18 Water bridges: A:R.196, A:R.196, A:S.248, B:Y.18, B:K.400, B:K.400, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.3: 4 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, B:R.196 Water bridges: A:E.149, A:F.399, A:K.400, A:K.415, A:K.415 Salt bridges: A:R.392, A:K.400 PO4.4: 5 residues within 4Å: Chain A: G.353, G.383, G.384, G.385 Chain B: R.392 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.353, A:G.383, A:G.384, A:G.385, B:R.392 Water bridges: A:V.356, A:V.356, B:R.392 PO4.6: 4 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.398, A:R.196 Water bridges: B:R.392, B:F.399, B:K.400, B:K.415, B:K.415 Salt bridges: B:R.392, B:K.400 PO4.7: 6 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.247, B:D.313, A:Y.18, A:Y.18 Water bridges: B:R.196, B:R.196, B:R.196, B:H.247, B:S.248, B:R.311, B:R.311, A:K.400 Salt bridges: B:R.196, B:H.247, B:R.311 PO4.8: 3 residues within 4Å: Chain A: R.392 Chain B: G.383, G.384 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.383, B:G.384 Water bridges: B:G.353, B:G.353, B:D.354, B:V.356, B:V.356, A:R.392, A:R.392 Salt bridges: A:R.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, M. et al., Discovery of a novel NAMPT inhibitor that selectively targets NAPRT-deficient EMT-subtype cancer cells and alleviates chemotherapy-induced peripheral neuropathy. Theranostics (2023)

Release Date

2023-10-11

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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