SMTL ID : 4o0z.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 2.05 Å

Oligo State

homo-dimer

Ligands

2 x 2RM: N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}indolizine-6-carboxamide(Non-covalent)

2RM.1: 18 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, P.273, S.275, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 Ligands: PO4.2 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.193, A:F.193, A:V.242, A:V.242, A:I.309, A:I.351 Hydrogen bonds: A:D.219, A:S.275 pi-Stacking: A:H.191, A:F.193, A:F.193, B:Y.18 Halogen bonds: A:Y.240 2RM.4: 16 residues within 4Å: Chain A: Y.18 Chain B: 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, A.379 Ligands: PO4.6 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.193, B:V.242, B:V.242 Hydrogen bonds: B:D.219 Water bridges: B:R.311 pi-Stacking: B:H.191, B:F.193, B:F.193, A:Y.18 Halogen bonds: B:Y.240

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

PO4.2: 7 residues within 4Å: Chain A: E.246, H.247, V.277, R.311, D.313 Chain B: Y.18 Ligands: 2RM.1 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.196, A:H.247, B:Y.18 Water bridges: A:R.196, A:R.196, A:S.248, A:R.311, A:R.311, B:K.400, B:K.400 Salt bridges: A:H.247, A:R.311 PO4.3: 5 residues within 4Å: Chain A: R.40, R.392, S.398, K.400 Chain B: R.196 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.40, A:S.398, A:S.398, B:R.196 Water bridges: A:F.399, A:K.415, A:K.415, A:K.415, A:K.415, A:K.423 Salt bridges: A:R.392, A:K.400, A:K.415 PO4.5: 6 residues within 4Å: Chain A: R.196 Chain B: R.40, R.392, S.398, K.400, K.415 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.40, B:S.398, A:R.196 Water bridges: B:R.40, B:R.40, B:R.392, B:R.392, B:K.415, B:K.423, B:K.423, B:K.423, A:D.354, A:D.354 Salt bridges: B:R.392, B:K.400, B:K.415 PO4.6: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: 2RM.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.247, B:D.313 Water bridges: B:R.196, B:R.196, B:R.196, B:S.248, B:R.311 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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