SMTL ID : 8c25.1 (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: 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 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:F.153 Hydrogen bonds: A:S.36, A:R.88, A:A.120, A:E.189, A:S.208, A:N.231, A:N.231 Water bridges: A:A.120, A:E.189, A:E.189, A:S.208 JU9.9: 21 residues within 4Å: 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, L.241, H.243, V.246 Chain C: F.153 12 PLIP interactions: 1 interactions with chain C, 11 interactions with chain B Hydrophobic interactions: C:F.153 Hydrogen bonds: B:S.36, B:R.88, B:A.120, B:E.189, B:S.208, B:N.231, B:N.231 Water bridges: B:A.120, B:E.189, B:E.189, B:S.208 JU9.17: 21 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, L.241, H.243, V.246 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: 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:A.120, C:S.208

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: S.137, D.138, T.157, D.158, P.162, R.165 Chain C: P.191 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.158, A:D.158, A:R.165, A:R.165 Water bridges: A:S.137, A:S.137, A:D.138, A:L.156, A:D.158, A:D.158 GOL.7: 6 residues within 4Å: Chain A: L.142 Ligands: GOL.8, GOL.15, GOL.16, GOL.23, GOL.24 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.141, A:T.143 GOL.8: 9 residues within 4Å: Chain A: L.142, L.200 Chain C: M.196, L.200 Ligands: GOL.7, GOL.15, GOL.16, GOL.23, GOL.24 No protein-ligand interaction detected (PLIP) GOL.10: 7 residues within 4Å: Chain A: P.191 Chain B: S.137, D.138, T.157, D.158, P.162, R.165 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.158, B:D.158, B:R.165, B:R.165 Water bridges: B:S.137, B:S.137, B:D.138, B:L.156, B:D.158, B:D.158 GOL.15: 6 residues within 4Å: Chain B: L.142 Ligands: GOL.7, GOL.8, GOL.16, GOL.23, GOL.24 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.141, B:T.143 GOL.16: 9 residues within 4Å: Chain A: M.196, L.200 Chain B: L.142, L.200 Ligands: GOL.7, GOL.8, GOL.15, GOL.23, GOL.24 No protein-ligand interaction detected (PLIP) GOL.18: 7 residues within 4Å: Chain B: P.191 Chain C: S.137, D.138, T.157, D.158, P.162, R.165 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.158, C:R.165, C:R.165 Water bridges: C:S.137, C:S.137, C:D.138, C:L.156, C:D.158, C:D.158 GOL.23: 6 residues within 4Å: Chain C: L.142 Ligands: GOL.7, GOL.8, GOL.15, GOL.16, GOL.24 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.141, C:T.143 GOL.24: 9 residues within 4Å: Chain B: M.196, L.200 Chain C: L.142, L.200 Ligands: GOL.7, GOL.8, GOL.15, GOL.16, GOL.23 No protein-ligand interaction detected (PLIP)

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

CL.3: 4 residues within 4Å: Chain A: S.36, G.37, L.39, P.40 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: G.35, S.36, G.87, R.88, H.90 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: N.231, L.232 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: S.36, G.37, L.39, P.40 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: G.35, S.36, G.87, R.88, H.90 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: N.231, L.232 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: S.36, G.37, L.39, P.40 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: 2 residues within 4Å: Chain C: N.231, L.232 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: V.100, E.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.212 NA.14: 2 residues within 4Å: Chain B: V.100, E.212 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.212 NA.22: 2 residues within 4Å: Chain C: V.100, E.212 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.100

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
A

B
A

C
A

Purine nucleoside phosphorylase

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