SMTL ID : 7zsn.1

human purine nucleoside phosphorylase in complex with JS-379

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

monomer

Ligands

1 x JSI: [(~{E})-2-[5-bromanyl-2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]phenyl]ethenyl]phosphonic acid(Non-covalent)

JSI.1: 19 residues within 4Å: Chain A: G.32, S.33, R.84, H.86, N.115, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, V.245, V.260, L.261 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.116, A:F.200 Hydrogen bonds: A:S.33, A:S.33, A:R.84, A:H.86, A:A.116, A:E.201, A:S.220, A:T.242, A:N.243, A:N.243 Water bridges: A:M.219 pi-Stacking: A:F.200

3 x TEW: 6-tungstotellurate(VI)(Non-covalent)

TEW.2: 2 residues within 4Å: Chain A: Q.144, R.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.144, A:R.148 TEW.3: 4 residues within 4Å: Chain A: R.207, D.248, Y.249, E.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.207, A:R.207, A:Y.249, A:E.250 TEW.4: 5 residues within 4Å: Chain A: N.55, F.56, P.57, R.58, K.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.55, A:R.58, A:R.58, A:K.95, A:K.95

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: S.33, G.34, L.35, G.36, Q.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.34, A:G.36, A:Q.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skacel, J. et al., Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Purine Nucleoside Phosphorylase Inhibitors. J.Med.Chem. (2023)

Release Date

2023-05-17

Peptides

Purine nucleoside phosphorylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Purine nucleoside phosphorylase

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