SMTL ID : 6hk6.1 (4 other biounits)

Human RIOK2 bound to inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x G8H: 2-naphthalen-2-yl-~{N}-pyridin-2-yl-ethanamide(Non-covalent)

G8H.1: 11 residues within 4Å: Chain A: V.5, M.102, I.112, A.122, M.189, E.190, L.191, I.192, G.194, I.236, I.246 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.5, A:M.102, A:I.112, A:A.122, A:I.236, A:I.246 Hydrogen bonds: A:I.192, A:I.192 G8H.7: 10 residues within 4Å: Chain B: M.102, I.112, A.122, M.189, E.190, L.191, I.192, G.194, I.236, I.246 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:M.102, B:I.112, B:A.122, B:I.236, B:I.246 Hydrogen bonds: B:I.192, B:I.192

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

CL.2: 2 residues within 4Å: Chain A: R.15, R.19 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: M.13, R.15 Ligand excluded by PLIP

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

EDO.4: 4 residues within 4Å: Chain A: D.82, L.86, V.98, Y.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.82 EDO.5: 2 residues within 4Å: Chain A: N.78, W.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.78 Water bridges: A:N.78 EDO.6: 5 residues within 4Å: Chain A: G.105, S.108, D.109, R.130 Chain B: P.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.108, A:R.130, A:R.130 EDO.9: 4 residues within 4Å: Chain B: D.82, L.86, V.98, Y.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.82, B:D.82 EDO.10: 6 residues within 4Å: Chain A: C.269, D.272 Chain B: W.261, D.264, R.265, K.268 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.268, A:D.272 Water bridges: B:E.260, B:D.264 EDO.11: 6 residues within 4Å: Chain A: W.261, D.264, K.268 Chain B: C.269, D.272, K.276 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.272, A:D.264, A:K.268

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 5 residues within 4Å: Chain B: R.172, H.223, E.294, D.295, T.296 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.295, B:D.295 Salt bridges: B:D.295, B:D.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Crystal structure of human RIOK2 bound to a specific inhibitor. Open Biology (2019)

Release Date

2018-10-24

Peptides

Serine/threonine-protein kinase RIO2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine/threonine-protein kinase RIO2

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