SMTL ID : 5lx5.1

CRYSTAL STRUCTURE OF VISFATIN IN COMPLEX WITH SAR154782-RP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x 7A0: [(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-5-[[[4-[6-(ethylamino)-5-(2-piperidin-1-ylethylcarbamoyl)pyridin-2-yl]-2-fluoranyl-phenyl]carbamoylamino]methyl]pyridin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

7A0.1: 24 residues within 4Å: Chain A: Y.190, H.193, F.195, R.198, D.221, S.243, V.244, A.246, S.277, T.306, I.311, R.313, D.315, R.351, V.352, I.353, I.380, A.381, G.385, G.386 Chain B: D.18, Y.20, R.394 Ligands: DPO.4 34 PLIP interactions: 28 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.190, A:D.221, A:V.244, A:I.311, A:R.351, A:I.353, A:A.381 Hydrogen bonds: A:R.198, A:S.277, A:R.313, A:R.313, A:D.315, A:D.315, A:G.385, A:G.386, B:D.18 Water bridges: A:Y.190, A:K.191, A:D.221, A:S.243, A:D.356, A:D.356, A:D.356, A:D.356, A:D.356, A:G.387, B:Y.20, B:R.394, B:R.394 pi-Stacking: A:F.195, B:Y.20 Halogen bonds: A:D.221, A:S.243 Salt bridges: B:R.394 7A0.3: 24 residues within 4Å: Chain A: D.18, Y.20, R.394 Chain B: Y.190, H.193, F.195, R.198, D.221, S.243, V.244, A.246, S.277, T.306, I.311, R.313, D.315, R.351, V.352, I.353, I.380, A.381, G.385, G.386 Ligands: DPO.2 31 PLIP interactions: 22 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:Y.190, B:D.221, B:V.244, B:I.311, B:R.351, B:I.353, B:A.381 Hydrogen bonds: B:R.198, B:S.277, B:R.313, B:R.313, B:D.315, B:D.315, B:G.385, B:G.386, A:D.18, A:Y.20 Water bridges: B:Y.190, B:K.191, B:D.221, B:S.243, A:R.394, A:R.394, A:R.394, A:R.394, A:R.394 pi-Stacking: B:F.195, A:Y.20 Halogen bonds: B:D.221, B:S.243 Salt bridges: A:R.394

2 x DPO: DIPHOSPHATE(Non-covalent)

DPO.2: 8 residues within 4Å: Chain A: R.42, R.394, S.400, K.402, K.417, K.425 Chain B: R.198 Ligands: 7A0.3 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.400 Water bridges: A:R.42, A:E.151, A:R.394, A:F.401, A:K.402, A:K.402, A:K.417, A:K.425, A:K.425, A:K.425, A:K.425, A:K.425, B:R.198, B:R.198 Salt bridges: A:R.42, A:R.394, A:K.402, A:K.402, A:K.417, A:K.425, B:R.198 DPO.4: 9 residues within 4Å: Chain A: R.198, D.315 Chain B: R.42, R.394, S.400, K.402, K.417, K.425 Ligands: 7A0.1 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.400 Water bridges: B:R.42, B:E.151, B:C.399, B:F.401, B:K.425, B:K.425, A:R.198, A:R.198, A:H.249, A:D.356 Salt bridges: B:R.42, B:R.394, B:K.402, B:K.402, B:K.417, B:K.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertrand, T. et al., CRYSTAL STRUCTURE OF VISFATIN IN COMPLEX WITH SAR154782-RP. To Be Published

Release Date

2017-10-25

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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