SMTL ID : 7zsr.1

purine nucleoside phosphorylase in complex with JS-379

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-trimer

Ligands

3 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: 20 residues within 4Å: Chain A: G.35, S.36, R.88, H.90, N.119, A.120, A.121, G.122, Y.188, E.189, V.205, G.206, M.207, S.208, T.230, N.231, H.243, V.246, L.247 Chain B: F.153 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.246 Hydrogen bonds: A:S.36, A:R.88, A:H.90, A:A.120, A:G.122, A:E.189, A:S.208, A:N.231, A:N.231 Water bridges: A:E.189, A:E.189, A:S.208 pi-Stacking: A:Y.188, B:F.153 JSI.4: 19 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.92, B:Y.188 Hydrogen bonds: B:S.36, B:R.88, B:H.90, B:A.120, B:E.189, B:S.208, B:N.231, B:N.231 Water bridges: B:E.189, B:M.207 pi-Stacking: B:Y.188, B:Y.188 JSI.6: 21 residues within 4Å: Chain A: F.153 Chain C: G.35, S.36, R.88, H.90, 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, L.247 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.246, A:F.153 Hydrogen bonds: C:S.36, C:R.88, C:A.120, C:E.189, C:S.208, C:N.231, C:N.231 Water bridges: C:N.119, C:M.207 pi-Stacking: C:Y.188

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 3 residues within 4Å: Chain A: T.143, R.145 Chain B: A.144 No protein-ligand interaction detected (PLIP) ACT.3: 2 residues within 4Å: Chain C: L.142, A.144 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.144 ACT.5: 8 residues within 4Å: Chain B: A.91, V.100, M.207, S.208, T.209, V.210, H.211, E.212 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.91 Water bridges: B:I.89, B:Y.92, B:T.209 Salt bridges: B:H.211

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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