SMTL ID : 7zsp.1

human purine nucleoside phosphorylase in complex with JS-555

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-trimer

Ligands

3 x JT3: [(~{E})-2-[2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]-6-[2,3,4,5,6-pentakis(fluoranyl)phenoxy]phenyl]ethenyl]phosphonic acid(Non-covalent)

JT3.1: 22 residues within 4Å: Chain A: 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 Chain B: F.159 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.116, A:F.200, A:F.200, B:F.159, B:F.159 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 Water bridges: A:E.201, A:E.201, A:M.219 pi-Stacking: A:F.200 Halogen bonds: A:H.257 JT3.6: 22 residues within 4Å: Chain B: 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 Chain C: F.159 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.116, B:F.200, B:F.200, C:F.159, 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:E.201, B:E.201, B:M.219 pi-Stacking: B:F.200 Halogen bonds: B:H.257 JT3.11: 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 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.116, C:F.200, C:F.200, A:F.159, A:F.159 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 Water bridges: C:E.201, C:E.201, C:M.219 pi-Stacking: C:F.200 Halogen bonds: C:H.257

9 x TEW: 6-tungstotellurate(VI)(Non-covalent)

TEW.2: 6 residues within 4Å: Chain A: Y.5, N.55, F.56, P.57, R.58, K.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.5, A:Y.5, A:R.58, A:K.95, A:K.95 TEW.3: 5 residues within 4Å: Chain A: R.207, D.248, Y.249, E.250 Chain B: R.133 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.207, A:R.207, A:Y.249, A:E.250, B:R.133, B:R.133 TEW.4: 9 residues within 4Å: Chain A: P.92, W.94, Q.144, R.148 Chain C: G.90, P.92, Q.144 Ligands: TEW.9, TEW.14 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.144, A:R.148, A:R.148, C:G.90, C:Q.144 TEW.7: 6 residues within 4Å: Chain B: Y.5, N.55, F.56, P.57, R.58, K.95 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.5, B:Y.5, B:R.58, B:K.95, B:K.95 TEW.8: 5 residues within 4Å: Chain B: R.207, D.248, Y.249, E.250 Chain C: R.133 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.207, B:R.207, B:Y.249, B:E.250, C:R.133, C:R.133 TEW.9: 9 residues within 4Å: Chain A: G.90, P.92, Q.144 Chain B: P.92, W.94, Q.144, R.148 Ligands: TEW.4, TEW.14 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.144, B:R.148, B:R.148, A:G.90, A:Q.144 TEW.12: 6 residues within 4Å: Chain C: Y.5, N.55, F.56, P.57, R.58, K.95 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.5, C:Y.5, C:R.58, C:K.95, C:K.95 TEW.13: 5 residues within 4Å: Chain A: R.133 Chain C: R.207, D.248, Y.249, E.250 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.207, C:R.207, C:Y.249, C:E.250, A:R.133, A:R.133 TEW.14: 9 residues within 4Å: Chain B: G.90, P.92, Q.144 Chain C: P.92, W.94, Q.144, R.148 Ligands: TEW.4, TEW.9 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.90, B:Q.144, C:Q.144, C:R.148, C:R.148

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

NA.5: 2 residues within 4Å: Chain A: T.6, E.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.6, A:T.6 NA.10: 2 residues within 4Å: Chain B: T.6, E.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.6, B:E.8 NA.15: 2 residues within 4Å: Chain C: T.6, E.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.6, C:T.6

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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