SMTL ID : 8c25.2 (1 other biounit)

purine nucleoside phosphorylase in complex with JS-375

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-trimer

Ligands

3 x JU9: [(~{E})-2-[4-methoxy-2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]phenyl]ethenyl]phosphonic acid(Non-covalent)

JU9.1: 19 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, H.243 Chain C: F.153 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.36, A:R.88, A:H.90, A:A.120, A:E.189, A:S.208, A:S.208, A:N.231, A:N.231 Water bridges: A:S.208 pi-Stacking: A:Y.188 Hydrophobic interactions: C:F.153 JU9.8: 19 residues within 4Å: Chain A: F.153 Chain B: 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, H.243 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:F.153 Hydrogen bonds: B:S.36, B:R.88, B:H.90, B:A.120, B:E.189, B:S.208, B:S.208, B:N.231, B:N.231 Water bridges: B:S.208 pi-Stacking: B:Y.188 JU9.15: 19 residues within 4Å: Chain B: 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, H.243 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.36, C:R.88, C:H.90, C:A.120, C:E.189, C:S.208, C:S.208, C:N.231, C:N.231 Water bridges: C:S.208 pi-Stacking: C:Y.188 Hydrophobic interactions: B:F.153

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: S.137, D.138, T.157, D.158, Y.160, P.162, R.165 Chain B: P.191 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.158, A:R.165, A:R.165 Water bridges: A:S.137, A:D.138, A:L.156, A:D.158, A:D.158 GOL.3: 6 residues within 4Å: Chain A: Q.129, V.130, G.131, Q.132, P.133, R.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.129, A:V.130, A:R.256 GOL.9: 8 residues within 4Å: Chain B: S.137, D.138, T.157, D.158, Y.160, P.162, R.165 Chain C: P.191 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.158, B:R.165, B:R.165 Water bridges: B:S.137, B:D.138, B:L.156, B:D.158, B:D.158 GOL.10: 6 residues within 4Å: Chain B: Q.129, V.130, G.131, Q.132, P.133, R.256 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.129, B:V.130, B:R.256 GOL.16: 8 residues within 4Å: Chain A: P.191 Chain C: S.137, D.138, T.157, D.158, Y.160, P.162, R.165 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.158, C:D.158, C:R.165, C:R.165 Water bridges: C:S.137, C:D.138, C:L.156, C:D.158, C:D.158 GOL.17: 6 residues within 4Å: Chain C: Q.129, V.130, G.131, Q.132, P.133, R.256 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.129, C:V.130, C:R.256

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: N.231, L.232, T.237 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: S.36, G.37, L.39, P.40, L.247 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: G.35, S.36, G.87, R.88, H.90 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: S.161, P.162, R.163 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: N.231, L.232, T.237 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: S.36, G.37, L.39, P.40, L.247 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: G.35, S.36, G.87, R.88, H.90 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: S.161, P.162, R.163 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: N.231, L.232, T.237 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain C: S.36, G.37, L.39, P.40, L.247 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain C: G.35, S.36, G.87, R.88, H.90 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: S.161, P.162, R.163 Ligand excluded by 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

2023-05-31

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

Purine nucleoside phosphorylase

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