SMTL ID : 4l4m.1

Structural Analysis of a Phosphoribosylated Inhibitor in Complex with Human Nicotinamide Phosphoribosyltransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x 1XD: N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}imidazo[1,2-a]pyridine-7-carboxamide(Non-covalent)

1XD.1: 17 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, Y.240, V.242, A.244, P.273, S.275, I.309, R.311, I.351, A.379 Chain B: Y.18 Ligands: PO4.2, EDO.4 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.191, A:F.193, A:V.242, A:V.242, A:I.309, A:I.351 Hydrogen bonds: A:R.196, A:D.219 Water bridges: A:R.311 pi-Stacking: A:H.191, A:F.193, B:Y.18 Halogen bonds: A:Y.240 1XD.5: 15 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, V.242, A.244, P.273, S.275, I.309, R.311, I.351 Ligands: PO4.7 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.193, B:V.242, B:V.242, B:I.309, B:I.351 Hydrogen bonds: B:D.219, B:R.311, B:R.311 pi-Stacking: B:H.191, B:F.193, A:Y.18

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

PO4.2: 8 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: 1XD.1, EDO.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.247, A:D.313, B:Y.18 Water bridges: A:H.247, A:D.313 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.3: 4 residues within 4Å: Chain A: R.40, R.392, S.398, K.400 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.398, A:S.398, A:S.398 Water bridges: A:R.392, A:R.392, A:K.400, A:K.400, A:K.415 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.6: 5 residues within 4Å: Chain B: R.40, R.392, S.398, K.400 Ligands: EDO.4 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.398, A:R.196 Water bridges: B:K.400, B:K.400 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415 PO4.7: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: 1XD.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.247 Water bridges: B:H.247, B:R.311, A:K.415 Salt bridges: B:R.196, B:H.247, B:R.311

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 8 residues within 4Å: Chain A: R.311, D.313, G.353, D.354 Chain B: K.423 Ligands: 1XD.1, PO4.2, PO4.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.423, A:R.311 EDO.8: 9 residues within 4Å: Chain A: H.247, S.248, T.251 Chain B: K.400, C.401, V.413, F.414, K.415, S.425 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:E.246, A:S.248, B:S.425, B:S.425 Hydrogen bonds: B:C.401

Links

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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

2014-06-11

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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