SMTL ID : 7zsl.1 (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: 20 residues within 4Å: Chain A: S.33, R.84, H.86, Y.88, 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, V.260 Chain B: F.159 14 PLIP interactions: 2 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:F.159, B:F.159 Hydrogen bonds: A:S.33, 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:M.219, A:M.219 pi-Stacking: A:F.200 JTO.6: 19 residues within 4Å: Chain B: S.33, R.84, H.86, Y.88, 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 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.200, C:F.159, C:F.159, C:F.159 Hydrogen bonds: B:S.33, B:R.84, B:H.86, B:H.86, B:A.116, B:E.201, B:N.243, B:N.243 Water bridges: B:E.201, B:E.201, B:M.219, B:M.219 pi-Stacking: B:F.200 JTO.9: 19 residues within 4Å: Chain A: F.159 Chain C: S.33, R.84, H.86, Y.88, 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 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.200, C:F.200, A:F.159, A: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:H.86, C:E.201, C:E.201, C:M.219, C:M.219 pi-Stacking: C:F.200

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

EDO.2: 8 residues within 4Å: Chain A: G.119, L.120, N.121, P.122, F.124, K.244, V.245, M.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.120, A:F.124, A:V.245 EDO.7: 5 residues within 4Å: Chain A: H.257 Chain B: E.153, D.157, R.158, F.159 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.153, B:R.158, B:F.159 Water bridges: B:F.159, A:H.257

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

SO4.3: 3 residues within 4Å: Chain A: P.92, Q.144 Chain B: R.148 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.144 Water bridges: A:L.93, B:R.148, B:R.148 Salt bridges: B:R.148 SO4.5: 2 residues within 4Å: Chain A: T.43, Q.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.44 Water bridges: A:A.45, A:A.45 SO4.8: 3 residues within 4Å: Chain B: P.92, Q.144 Chain C: R.148 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Salt bridges: C:R.148 Hydrogen bonds: B:Q.144 Water bridges: B:L.93, B:L.93 SO4.11: 4 residues within 4Å: Chain A: R.148 Chain C: P.92, Q.144 Ligands: PEG.4 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.144 Water bridges: C:L.93, C:W.94 Salt bridges: A:R.148

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

PEG.4: 2 residues within 4Å: Chain A: N.3 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.3 PEG.10: 3 residues within 4Å: Chain C: E.258, E.259, A.262 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.262

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

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