SMTL ID : 7zsq.1

human purine nucleoside phosphorylase in complex with JS-555

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-trimer

Ligands

3 x JTO: [2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]phenoxy]methylphosphonic acid(Non-covalent)

JTO.1: 21 residues within 4Å: Chain A: G.35, S.36, R.88, H.90, Y.92, N.119, A.120, A.121, G.122, Y.188, E.189, V.205, G.206, M.207, S.208, T.230, N.231, L.241, H.243, V.246 Chain B: F.153 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.36, A:R.88, A:H.90, A:A.120, A:E.189, A:S.208, A:T.230, A:N.231, A:N.231 Water bridges: A:Y.188, A:M.207, A:S.208 pi-Stacking: A:Y.188 Hydrophobic interactions: B:F.153, B:F.153 JTO.4: 20 residues within 4Å: Chain B: G.35, S.36, H.68, R.88, H.90, Y.92, N.119, A.120, A.121, G.122, Y.188, E.189, V.205, G.206, M.207, S.208, T.230, N.231 Chain C: F.153 Ligands: EDO.6 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.188, C:F.153 Hydrogen bonds: B:S.36, B:S.36, B:S.36, B:H.68, B:R.88, B:A.120, B:E.189, B:T.230, B:N.231, B:N.231 Water bridges: B:E.189, B:E.189, B:M.207, B:M.207 JTO.7: 19 residues within 4Å: Chain A: F.153 Chain C: G.35, S.36, R.88, H.90, Y.92, N.119, A.120, A.121, G.122, Y.188, E.189, V.205, G.206, M.207, S.208, T.230, N.231 Ligands: PEG.8 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.92, C:Y.188, A:F.153 Hydrogen bonds: C:S.36, C:R.88, C:H.90, C:A.120, C:E.189, C:S.208, C:T.230, C:N.231, C:N.231 Water bridges: C:M.207, C:S.208 pi-Stacking: C:Y.188

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

TEW.2: 11 residues within 4Å: Chain A: S.36, L.39, H.68, G.87, R.88, H.90, Y.92, E.93, H.243 Chain B: G.151, F.153 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:G.150 Hydrogen bonds: A:S.36, A:R.88, A:H.90, A:E.93, A:H.243

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: A.144, R.145 Chain B: A.144 Chain C: A.144, R.145 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:A.144, B:A.144, C:A.144

1 x P4K: polyethylene glycol(Non-covalent)

P4K.5: 8 residues within 4Å: Chain A: L.142, M.196, L.200 Chain B: L.142, A.144, M.196 Chain C: L.142, A.144 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.142 Water bridges: C:N.141

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

EDO.6: 2 residues within 4Å: Chain B: Y.188 Ligands: JTO.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.188

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 6 residues within 4Å: Chain A: F.153 Chain C: S.36, A.120, Y.188, T.230 Ligands: JTO.7 No protein-ligand interaction detected (PLIP)

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Purine nucleoside phosphorylase