SMTL ID : 4o12.1

Structural and Biochemical Analyses of the Catalysis and Potency Impact of Inhibitor Phosphoribosylation by Human Nicotinamide Phosphoribosyltransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x 2QG: 2-[6-(4-chlorophenoxy)hexyl]-1-cyano-3-pyridin-4-ylguanidine(Non-covalent)

2QG.1: 15 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, S.275, I.309, R.311, I.351 Chain B: D.16, Y.18 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.188, A:F.193, A:V.242, A:I.309, A:I.351, B:D.16, B:Y.18, B:Y.18 Hydrogen bonds: A:D.219, A:S.241, A:S.275 Water bridges: A:R.311 pi-Stacking: A:F.193 2QG.3: 20 residues within 4Å: Chain A: Y.18 Chain B: K.189, 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, E.376, N.377, I.378, A.379 Ligands: PO4.5 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:F.193, B:I.309, B:R.349, B:I.351, B:A.379, B:A.379, A:Y.18, A:Y.18 Hydrogen bonds: B:D.219, B:S.275 Water bridges: B:A.245 pi-Stacking: B:F.193 Halogen bonds: B:E.376

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

PO4.2: 5 residues within 4Å: Chain A: R.40, R.392, S.398, K.400, K.423 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Water bridges: A:R.392, A:R.392, A:K.415, A:K.415, A:K.415, A:K.423, B:R.196 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.423 PO4.4: 4 residues within 4Å: Chain B: R.40, R.392, S.398, K.400 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Water bridges: A:D.313, A:D.313, A:D.313, A:D.354, B:K.400, B:K.400, B:K.415 Hydrogen bonds: B:S.398 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415, B:K.423 PO4.5: 8 residues within 4Å: Chain A: Y.18 Chain B: R.196, A.245, E.246, H.247, R.311, D.313 Ligands: 2QG.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.247 Water bridges: B:R.196, B:R.196, B:H.247, B:S.248, B:R.311, B:D.313 Salt bridges: B:R.196, B:H.247, B:R.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oh, A. et al., Structural and biochemical analyses of the catalysis and potency impact of inhibitor phosphoribosylation by human nicotinamide phosphoribosyltransferase. Chembiochem (2014)

Release Date

2014-06-18

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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