SMTL ID : 8dtj.1

Human NAMPT in complex with small molecule activator ZN-43-S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: R.40, R.392, S.398, K.400 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.398 Water bridges: A:R.392, A:R.392 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.4: 6 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, F.399, K.400 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:C.397, B:S.398, B:F.399 Water bridges: B:R.40, B:R.392, B:R.392, B:K.423 Salt bridges: B:R.40, B:R.392, B:K.400

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.123, V.124, R.434, F.440, N.479 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.124, A:V.124, A:R.434, A:N.479 GOL.5: 2 residues within 4Å: Chain B: K.469, S.470 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.469, B:S.470, B:S.470 GOL.6: 5 residues within 4Å: Chain B: F.123, V.124, R.434, F.440, N.479 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.124, B:R.434

2 x TKF: (3S)-N-[(1-benzothiophen-5-yl)methyl]-1-{2-[4-(trifluoromethyl)phenyl]-2H-pyrazolo[3,4-d]pyrimidin-4-yl}piperidine-3-carboxamide(Non-covalent)

TKF.3: 17 residues within 4Å: Chain A: D.184, G.185, Y.188, K.189, H.191, F.193, V.242, S.275, P.307, I.309, R.349, V.350, I.351, E.376, N.377, I.378, A.379 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.188, A:Y.188, A:I.309, A:R.349, A:R.349, A:I.351, A:A.379 Hydrogen bonds: A:K.189 TKF.7: 16 residues within 4Å: Chain B: D.184, G.185, Y.188, K.189, H.191, F.193, V.242, S.275, P.307, I.309, R.349, V.350, I.351, E.376, I.378, A.379 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.188, B:V.242, B:I.309, B:R.349, B:I.351, B:A.379 Hydrogen bonds: B:K.189

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

CL.8: 1 residues within 4Å: Chain B: G.384 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ratia, K.M. et al., Mechanism of Allosteric Modulation of Nicotinamide Phosphoribosyltransferase to Elevate Cellular NAD. Biochemistry (2023)

Release Date

2023-03-08

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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