SMTL ID : 5j4v.1

The crystal structure of Inhibitor Bound to JCV Helicase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.94 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.47, C.50, H.58, H.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.47, A:C.50, A:H.58, A:H.62 ZN.5: 4 residues within 4Å: Chain B: C.47, C.50, H.58, H.62 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.47, B:C.50, B:H.58, B:H.62 ZN.9: 4 residues within 4Å: Chain C: C.47, C.50, H.58, H.62 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.47, C:C.50, C:H.58, C:H.62 ZN.13: 4 residues within 4Å: Chain D: C.47, C.50, H.58, H.62 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.47, D:C.50, D:H.58, D:H.62 ZN.17: 4 residues within 4Å: Chain E: C.47, C.50, H.58, H.62 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.47, E:C.50, E:H.58, E:H.62 ZN.21: 4 residues within 4Å: Chain F: C.47, C.50, H.58, H.62 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.47, F:C.50, F:H.58, F:H.62

6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 6 residues within 4Å: Chain A: I.325, W.326, K.345, D.349, S.353, M.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.345, A:M.354 Salt bridges: A:D.349 MES.6: 6 residues within 4Å: Chain B: I.325, W.326, K.345, D.349, S.353, M.354 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.345, B:M.354 Salt bridges: B:D.349 MES.10: 6 residues within 4Å: Chain C: I.325, W.326, K.345, D.349, S.353, M.354 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.345, C:M.354 Salt bridges: C:D.349 MES.14: 6 residues within 4Å: Chain D: I.325, W.326, K.345, D.349, S.353, M.354 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.345, D:M.354 Salt bridges: D:D.349 MES.18: 6 residues within 4Å: Chain E: I.325, W.326, K.345, D.349, S.353, M.354 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.345, E:M.354 Salt bridges: E:D.349 MES.22: 6 residues within 4Å: Chain F: I.325, W.326, K.345, D.349, S.353, M.354 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.345, F:M.354 Salt bridges: F:D.349

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

SO4.3: 8 residues within 4Å: Chain A: D.174, S.175, G.176, K.177, T.178, T.179 Chain F: R.243 Ligands: 6JH.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:D.174, A:S.175, A:G.176, A:T.178, A:T.178, A:T.179, A:T.179, F:R.243 SO4.7: 8 residues within 4Å: Chain B: D.174, S.175, G.176, K.177, T.178, T.179 Chain D: R.243 Ligands: 6JH.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.174, B:S.175, B:G.176, B:T.178, B:T.178, B:T.179, B:T.179, D:R.243 SO4.11: 8 residues within 4Å: Chain C: D.174, S.175, G.176, K.177, T.178, T.179 Chain E: R.243 Ligands: 6JH.12 8 PLIP interactions: 1 interactions with chain E, 7 interactions with chain C Hydrogen bonds: E:R.243, C:D.174, C:S.175, C:G.176, C:T.178, C:T.178, C:T.179, C:T.179 SO4.15: 8 residues within 4Å: Chain C: R.243 Chain D: D.174, S.175, G.176, K.177, T.178, T.179 Ligands: 6JH.16 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.174, D:S.175, D:G.176, D:T.178, D:T.178, D:T.179, D:T.179, C:R.243 SO4.19: 8 residues within 4Å: Chain A: R.243 Chain E: D.174, S.175, G.176, K.177, T.178, T.179 Ligands: 6JH.20 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:D.174, E:S.175, E:G.176, E:T.178, E:T.178, E:T.179, E:T.179, A:R.243 SO4.23: 8 residues within 4Å: Chain B: R.243 Chain F: D.174, S.175, G.176, K.177, T.178, T.179 Ligands: 6JH.24 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:D.174, F:S.175, F:G.176, F:T.178, F:T.178, F:T.179, F:T.179, B:R.243

6 x 6JH: 2-(2-phenoxypyridin-3-yl)[1,3]thiazolo[5,4-c]pyridine(Non-covalent)

6JH.4: 15 residues within 4Å: Chain A: W.138, L.142, D.174, S.175, G.176, T.179, R.293, P.294, K.295, L.298, R.299, L.302, L.309 Chain F: K.163 Ligands: SO4.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:W.138, A:L.142, A:R.299, A:L.302, F:K.163 Hydrogen bonds: A:K.295 pi-Cation interactions: A:R.299 6JH.8: 15 residues within 4Å: Chain B: W.138, L.142, D.174, S.175, G.176, T.179, R.293, P.294, K.295, L.298, R.299, L.302, L.309 Chain D: K.163 Ligands: SO4.7 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:W.138, B:L.142, B:R.299, B:L.302, D:K.163 Hydrogen bonds: B:K.295 pi-Cation interactions: B:R.299 6JH.12: 15 residues within 4Å: Chain C: W.138, L.142, D.174, S.175, G.176, T.179, R.293, P.294, K.295, L.298, R.299, L.302, L.309 Chain E: K.163 Ligands: SO4.11 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:W.138, C:L.142, C:R.299, C:L.302, E:K.163 Hydrogen bonds: C:K.295 pi-Cation interactions: C:R.299 6JH.16: 15 residues within 4Å: Chain C: K.163 Chain D: W.138, L.142, D.174, S.175, G.176, T.179, R.293, P.294, K.295, L.298, R.299, L.302, L.309 Ligands: SO4.15 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.138, D:L.142, D:R.299, D:L.302, C:K.163 Hydrogen bonds: D:K.295 pi-Cation interactions: D:R.299 6JH.20: 15 residues within 4Å: Chain A: K.163 Chain E: W.138, L.142, D.174, S.175, G.176, T.179, R.293, P.294, K.295, L.298, R.299, L.302, L.309 Ligands: SO4.19 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:W.138, E:L.142, E:R.299, E:L.302, A:K.163 Hydrogen bonds: E:K.295 pi-Cation interactions: E:R.299 6JH.24: 15 residues within 4Å: Chain B: K.163 Chain F: W.138, L.142, D.174, S.175, G.176, T.179, R.293, P.294, K.295, L.298, R.299, L.302, L.309 Ligands: SO4.23 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:W.138, F:L.142, F:R.299, F:L.302, B:K.163 Hydrogen bonds: F:K.295 pi-Cation interactions: F:R.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonafoux, D. et al., Fragment-Based Discovery of Dual JC Virus and BK Virus Helicase Inhibitors. J.Med.Chem. (2016)

Release Date

2016-07-20

Peptides

Large T antigen: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Large T antigen

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