SMTL ID : 8f7l.1

Human NAMPT in complex with substrate NAM and small molecule activator ZN-29-S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x NCA: NICOTINAMIDE(Non-covalent)

NCA.1: 7 residues within 4Å: Chain A: F.193, R.196, D.219, A.244, R.311 Chain B: D.16, Y.18 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.219 pi-Stacking: A:F.193, B:Y.18 Hydrophobic interactions: B:D.16 NCA.5: 7 residues within 4Å: Chain A: D.16, Y.18 Chain B: F.193, R.196, D.219, A.244, R.311 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.219 Water bridges: B:R.311 pi-Stacking: B:F.193 Hydrophobic interactions: A:Y.18, A:Y.18

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

PO4.2: 6 residues within 4Å: Chain A: R.40, R.392, S.398, K.400, K.415, K.423 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.40, A:S.398, A:S.398 Water bridges: A:K.415 Salt bridges: A:R.392, A:K.400, A:K.415, A:K.423 PO4.6: 5 residues within 4Å: Chain B: R.40, R.392, S.398, K.400, K.415 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.398, B:S.398 Water bridges: B:R.392, B:R.392, B:R.392, B:F.399, B:K.400, B:K.400, B:K.415, A:R.196 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415

2 x XI3: (3S)-N-[(1-benzothiophen-5-yl)methyl]-1-[(2P)-2-(3-fluoro-4-methylphenyl)-2H-pyrazolo[3,4-d]pyrimidin-4-yl]piperidine-3-carboxamide(Non-covalent)

XI3.3: 12 residues within 4Å: Chain A: G.185, Y.188, K.189, H.191, V.242, P.307, I.309, R.349, V.350, I.351, I.378, A.379 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.188, A:V.242, A:P.307, A:I.309, A:I.351, A:A.379 Hydrogen bonds: A:K.189 XI3.7: 13 residues within 4Å: Chain B: D.184, G.185, Y.188, K.189, H.191, P.307, I.309, R.349, V.350, I.351, E.376, I.378, A.379 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.188, B:P.307, B:I.309, B:R.349, B:A.379 Hydrogen bonds: B:K.189

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: T.76, K.77, L.105 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ratia, K. et al., Human NAMPT in complex with substrate NAM and small molecule activator ZN-29-S. To Be Published

Release Date

2023-11-29

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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