SMTL ID : 6pjj.1

Human PRPF4B bound to benzothiophene inhibitor 224

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x OCJ: 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide(Non-covalent)

OCJ.1: 12 residues within 4Å: Chain A: T.39, V.47, A.61, K.63, E.78, L.97, F.113, L.116, N.119, E.122, L.168, D.180 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.39, A:V.47, A:A.61, A:E.122, A:L.168, A:L.168 Hydrogen bonds: A:T.39, A:E.122, A:D.180, A:D.180 Water bridges: A:F.181 OCJ.6: 17 residues within 4Å: Chain B: T.39, G.40, V.47, A.61, K.63, E.78, L.97, F.113, L.116, S.117, M.118, N.119, E.122, L.168, C.179, D.180 Chain D: S.293 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.39, B:V.47, B:V.47, B:A.61, B:F.113, B:L.168, B:L.168 Hydrogen bonds: B:T.39, B:E.122, B:D.180, B:D.180 Water bridges: B:N.119 OCJ.12: 16 residues within 4Å: Chain C: T.39, G.40, V.47, A.61, K.63, E.78, L.97, F.113, L.116, S.117, M.118, N.119, E.122, L.168, C.179, D.180 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.47, C:A.61, C:F.113, C:L.168, C:L.168 Hydrogen bonds: C:T.39, C:E.122, C:D.180, C:D.180 Water bridges: C:F.181 OCJ.16: 14 residues within 4Å: Chain D: T.39, G.40, A.61, K.63, E.78, L.97, F.113, L.116, M.118, N.119, E.122, L.168, C.179, D.180 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:T.39, D:A.61, D:E.122, D:L.168 Hydrogen bonds: D:T.39, D:E.122, D:D.180, D:D.180

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: L.85, N.86, D.89, D.92, F.94, H.95, C.96, R.98, L.151 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.85, A:N.86, A:D.92, A:D.92, A:F.94, A:C.96, A:R.98 EDO.8: 7 residues within 4Å: Chain B: A.137, S.140, Y.141, K.173, T.174 Chain C: D.87, A.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.140, B:S.140 EDO.9: 2 residues within 4Å: Chain B: Y.141, K.173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.141 EDO.10: 4 residues within 4Å: Chain B: L.250, K.251, K.323, D.327 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.250, B:K.251, B:K.323, B:K.323 EDO.15: 4 residues within 4Å: Chain C: L.250, K.251, K.323, D.327 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.251, C:K.251, C:K.323, C:K.323 EDO.17: 9 residues within 4Å: Chain D: L.85, N.86, D.89, D.92, F.94, H.95, C.96, R.98, L.151 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:L.85, D:N.86, D:D.92, D:D.92, D:F.94, D:C.96 EDO.18: 5 residues within 4Å: Chain D: R.199, F.200, P.236, G.237, K.238 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.199 EDO.20: 3 residues within 4Å: Chain D: Y.195, R.199, R.202 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.199, D:R.202, D:R.202

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: R.32, R.55, R.101 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.32, A:R.55, A:R.101 PO4.4: 3 residues within 4Å: Chain A: R.101 Chain B: R.49 Ligands: PO4.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.101, B:R.49 PO4.5: 3 residues within 4Å: Chain A: Y.195, R.199, R.202 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.199, A:R.199, A:N.240 Salt bridges: A:R.199, A:R.202 PO4.7: 4 residues within 4Å: Chain B: Y.195, R.199, R.202, N.240 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.199, B:N.240 Salt bridges: B:R.199, B:R.202 PO4.11: 2 residues within 4Å: Chain B: R.32, R.101 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.32, B:R.101 PO4.13: 3 residues within 4Å: Chain B: K.317 Chain C: R.32, R.101 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.32, C:R.101, B:K.317 PO4.14: 3 residues within 4Å: Chain C: Y.195, R.199, R.202 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.240 Salt bridges: C:R.199, C:R.202 PO4.19: 3 residues within 4Å: Chain D: R.32, R.55, R.101 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.32, D:R.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godoi, P.H.C. et al., to be published. To Be Published

Release Date

2019-08-28

Peptides

Serine/threonine-protein kinase PRP4 homolog: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine/threonine-protein kinase PRP4 homolog

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