SMTL ID : 7zsl.2 (1 other biounit)

human purine nucleoside phosphorylase in complex with JS-196

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: 17 residues within 4Å: Chain A: 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, H.257 Chain C: F.159 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.200, A:F.200, C:F.159, C:F.159 Hydrogen bonds: A:R.84, A:H.86, A:H.86, A:A.116, A:E.201, A:N.243, A:N.243 Water bridges: A:E.201, A:E.201, A:M.219, A:M.219 pi-Stacking: A:F.200 JTO.5: 18 residues within 4Å: Chain A: F.159 Chain B: 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, H.257 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.200, A:F.159, A:F.159 Hydrogen bonds: B:S.33, B:S.33, B:R.84, B:H.86, B:A.116, B:E.201, B:S.220, B:N.243, B:N.243 Water bridges: B:E.201, B:M.219 pi-Stacking: B:F.200 JTO.7: 17 residues within 4Å: Chain B: F.159 Chain C: 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, H.257 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.200, C:F.200, B:F.159, B:F.159 Hydrogen bonds: C:S.33, C:S.33, C:R.84, C:A.116, C:E.201, C:N.243, C:N.243 Water bridges: C:E.201, C:E.201, C:M.219, C:M.219 pi-Stacking: C:F.200

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

SO4.2: 3 residues within 4Å: Chain A: P.92, Q.144 Chain C: R.148 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Salt bridges: C:R.148 Hydrogen bonds: A:Q.144 Water bridges: A:L.93, A:L.93 SO4.3: 3 residues within 4Å: Chain A: R.148 Chain B: P.92, Q.144 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.144 Water bridges: B:L.93 Salt bridges: A:R.148 SO4.4: 5 residues within 4Å: Chain A: E.153, D.157, R.158, F.159 Chain B: H.257 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.158, A:F.159 Water bridges: B:H.257, B:H.257, B:E.258 Salt bridges: B:H.257 SO4.6: 3 residues within 4Å: Chain B: R.173, P.283, L.284 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.284 Salt bridges: B:R.173 SO4.10: 3 residues within 4Å: Chain C: R.173, P.283, L.284 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.282, C:L.284 Salt bridges: C:R.173 SO4.11: 2 residues within 4Å: Chain C: T.43, Q.44 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.44

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

PEG.8: 6 residues within 4Å: Chain A: N.256, H.257 Chain C: E.153, D.157, R.158, F.159 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.153, C:R.158, A:H.257

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

EDO.9: 4 residues within 4Å: Chain C: R.133, R.171, L.175, E.189 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.133, C:R.171, C:R.171

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
D

B
E

C
F

Purine nucleoside phosphorylase

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