SMTL ID : 4l4l.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

2 x 1XC: 6-({4-[(3,5-difluorophenyl)sulfonyl]benzyl}carbamoyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)imidazo[1,2-a]pyridin-1-ium(Non-covalent)

1XC.1: 24 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, P.273, S.275, I.309, R.311, D.313, I.351, G.353, A.379, G.383, G.384 Chain B: D.16, Y.18, R.392 Ligands: PO4.2, EDO.5, PO4.9 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.242, A:V.242, A:I.309 Hydrogen bonds: A:D.219, A:D.313, A:G.383, A:G.384 Water bridges: A:R.311, A:R.311, A:D.354, A:V.356, A:G.385, B:R.392, B:K.423 pi-Stacking: A:H.191, A:F.193, A:F.193, B:Y.18 Salt bridges: B:R.392 1XC.7: 23 residues within 4Å: Chain A: D.16, Y.18, R.392 Chain B: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, P.273, S.275, I.309, R.311, D.313, I.351, G.353, A.379, G.383, G.384 Ligands: PO4.3, PO4.8 17 PLIP interactions: 5 interactions with chain A, 12 interactions with chain B Water bridges: A:R.392, A:R.392, A:R.392, B:R.311, B:R.311 Salt bridges: A:R.392 pi-Stacking: A:Y.18, B:H.191, B:F.193, B:F.193 Hydrophobic interactions: B:V.242, B:V.242, B:I.309 Hydrogen bonds: B:D.219, B:D.313, B:G.383, B:G.384

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

PO4.2: 8 residues within 4Å: Chain A: R.196, A.245, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: 1XC.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.247, B:Y.18 Water bridges: A:R.196, A:R.196, A:R.196, A:S.248 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.3: 6 residues within 4Å: Chain A: R.40, R.392, S.398, K.400, K.415 Ligands: 1XC.7 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398, A:S.398 Water bridges: A:R.392, A:R.392, A:R.392, A:K.400, A:K.400, A:K.415, A:K.423, B:R.196 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415, A:K.423 PO4.8: 7 residues within 4Å: Chain A: Y.18 Chain B: E.246, H.247, V.277, R.311, D.313 Ligands: 1XC.7 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.247 Water bridges: B:R.196, B:R.196, B:S.248, A:Y.18, A:K.400 Salt bridges: B:H.247, B:R.311 PO4.9: 6 residues within 4Å: Chain B: R.40, R.392, S.398, K.400, K.415 Ligands: 1XC.1 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.398, B:S.398 Water bridges: B:R.392, B:K.415, B:K.415, B:K.423, B:K.423, A:R.196, A:D.313 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415, B:K.423

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

EDO.4: 5 residues within 4Å: Chain A: F.123, V.124, R.434, F.440, N.479 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.122, A:V.124, A:R.434 EDO.5: 6 residues within 4Å: Chain A: K.189, R.349, E.376, I.378, A.379 Ligands: 1XC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.189, A:K.189 EDO.6: 5 residues within 4Å: Chain A: P.27, P.28, N.29, T.30, Y.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.27, A:T.30

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

2014-06-11

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

Related Entries With Identical Sequence