SMTL ID : 7zsm.1

human purine nucleoside phosphorylase in complex with JS-375

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 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.32, S.33, R.84, H.86, Y.88, N.115, A.116, A.117, G.118, P.198, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, V.245, H.257 Chain B: F.159 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.33, A:R.84, A:A.116, A:E.201, A:S.220, A:T.242, A:N.243, A:N.243 Hydrophobic interactions: B:F.159 JU9.7: 21 residues within 4Å: Chain B: G.32, S.33, R.84, H.86, Y.88, N.115, A.116, A.117, G.118, P.198, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, V.245, H.257 Chain C: F.159 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.33, B:R.84, B:A.116, B:E.201, B:S.220, B:T.242, B:N.243, B:N.243 Hydrophobic interactions: C:F.159 JU9.13: 21 residues within 4Å: Chain A: F.159 Chain C: G.32, S.33, R.84, H.86, Y.88, N.115, A.116, A.117, G.118, P.198, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, V.245, H.257 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.33, C:R.84, C:A.116, C:E.201, C:S.220, C:T.242, C:N.243, C:N.243 Hydrophobic interactions: A:F.159

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

SO4.2: 3 residues within 4Å: Chain A: R.133 Chain C: R.207, Y.249 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.207, A:R.133 SO4.3: 4 residues within 4Å: Chain A: R.133, R.171, E.189 Chain C: Y.249 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.133, A:R.171 SO4.8: 3 residues within 4Å: Chain A: R.207, Y.249 Chain B: R.133 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.133, A:R.207 SO4.9: 4 residues within 4Å: Chain A: Y.249 Chain B: R.133, R.171, E.189 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.133, B:R.171 SO4.14: 3 residues within 4Å: Chain B: R.207, Y.249 Chain C: R.133 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.133, B:R.207 SO4.15: 4 residues within 4Å: Chain B: Y.249 Chain C: R.133, R.171, E.189 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.133, C:R.171

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

CL.4: 4 residues within 4Å: Chain A: R.148 Chain C: G.90, P.92 Ligands: CL.18 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: R.58 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: Q.144 Ligands: CL.10 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: G.90, P.92 Chain B: R.148 Ligands: CL.6 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: R.58 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: Q.144 Ligands: CL.16 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: G.90, P.92 Chain C: R.148 Ligands: CL.12 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain C: R.58 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: Q.144 Ligands: CL.4 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

2023-05-17

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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