SMTL ID : 7zso.1

human purine nucleoside phosphorylase in complex with JS-554

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

3 x JTC: [(~{E})-2-[2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]-5-[2,3,4,5,6-pentakis(fluoranyl)phenoxy]phenyl]ethenyl]phosphonic acid(Non-covalent)

JTC.1: 23 residues within 4Å: Chain A: G.32, S.33, G.34, R.84, H.86, 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, V.260, L.261, G.264 Chain B: F.159 Ligands: SO4.8 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.260 Hydrogen bonds: A:S.33, A:R.84, A:H.86, A:H.86, A:A.116, A:E.201, A:S.220, A:N.243, A:N.243 Water bridges: A:E.201, A:M.219 pi-Stacking: A:F.200, B:F.159 JTC.12: 23 residues within 4Å: Chain B: G.32, S.33, G.34, R.84, H.86, 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, L.261 Chain C: F.159 Ligands: SO4.15 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.116, B:F.200, B:V.260, C:F.159 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 Water bridges: B:N.115, B:E.201, B:E.201, B:M.219 JTC.16: 22 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, F.200, E.201, V.217, G.218, M.219, S.220, T.242, N.243, V.245, H.257, V.260, L.261 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.116, A:F.159 Hydrogen bonds: C:S.33, C:R.84, C:A.116, C:E.201, C:S.220, C:N.243, C:N.243 Water bridges: C:N.115, C:E.201, C:E.201, C:M.219 pi-Stacking: C:F.200 pi-Cation interactions: C:H.257 Halogen bonds: C:Y.88, C:H.257

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: L.42, T.43, Q.44, A.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.44, A:A.45 GOL.3: 8 residues within 4Å: Chain A: L.93, W.94, G.143, Q.144, N.145, P.146, R.148 Ligands: SO4.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.93, A:W.94, A:G.143, A:R.148 Water bridges: A:Q.144 GOL.17: 7 residues within 4Å: Chain C: L.93, W.94, G.143, Q.144, N.145, R.148 Ligands: SO4.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.93, C:W.94, C:N.145, C:R.148

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

SO4.4: 4 residues within 4Å: Chain A: R.133, R.168, R.171 Chain C: Y.249 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: P.57, R.58, K.95 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: R.173, P.283, L.284 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain A: R.168 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: G.32, S.33, G.34, L.35, G.36 Ligands: JTC.1 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: P.54, N.55, F.56 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: R.207, Y.249 Chain B: R.133 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: P.92, Q.144 Chain B: R.148 Ligands: GOL.3 Ligand excluded by PLIP SO4.14: 10 residues within 4Å: Chain A: L.138, F.141, S.142 Chain B: L.138, F.141, S.142 Chain C: L.138, F.141, S.142 Ligands: NA.11 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: S.33, G.34, L.35, G.36 Ligands: JTC.12 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: P.92, Q.144 Chain C: R.148 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: R.148 Chain C: P.92, Q.144 Ligands: GOL.17 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: I.53, P.54, N.55, F.56 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: R.173, P.283, L.284 Ligands: NA.26 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain B: Y.249 Chain C: R.133, R.168, R.171, E.189 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: T.6, Y.7, E.8, R.154 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain A: R.133 Chain C: R.207, Y.249 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: R.207, Y.249 Chain C: R.133 Ligand excluded by PLIP

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

NA.11: 1 residues within 4Å: Ligands: SO4.14 No protein-ligand interaction detected (PLIP) NA.26: 2 residues within 4Å: Chain C: R.173 Ligands: SO4.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.173

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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