SMTL ID : 4rlo.3 (2 other biounits)

Human p70s6k1 with ruthenium-based inhibitor EM5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

1 x 3T3: [(amino-kappaN)methanethiolato](3-fluoro-9-hydroxypyrido[2,3-a]pyrrolo[3,4-c]carbazole-5,7(6H,12H)-dionato-kappa~2~N,N')(1,4,7-trithionane-kappa~3~S~1~,S~4~,S~7~)ruthenium(Non-covalent)

3T3.1: 23 residues within 4Å: Chain A: R.11, L.13, G.14, K.15, G.16, G.19, K.20, V.21, A.37, K.39, E.59, V.72, L.88, E.89, Y.90, L.91, G.94, E.95, E.138, N.139, M.141, T.151, D.152 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:L.13 Hydrogen bonds: A:E.89, A:L.91 Salt bridges: A:E.95, A:E.138, A:D.152 Halogen bonds: A:K.39, A:E.59

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: D.109, C.112, F.113, H.270, I.271, V.281 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.270 GOL.8: 12 residues within 4Å: Chain B: K.39, Y.132, N.139, M.141, K.149, L.150, T.151, F.153, G.154, K.157 Ligands: STU.7, SO4.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.151, B:T.151, B:K.157 Water bridges: B:K.39, B:D.134, B:D.134 GOL.9: 9 residues within 4Å: Chain B: E.108, D.109, C.112, T.233, E.235, P.266, F.267, R.269, H.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.108, B:T.233, B:R.269

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

CL.3: 2 residues within 4Å: Chain A: N.187, R.188 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: R.269, H.270 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: P.230, L.232, T.233, Q.234, R.237 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: R.269, H.270 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: N.187, R.188 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: R.25, G.33, I.35 Ligand excluded by PLIP

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

SO4.6: 4 residues within 4Å: Chain A: R.11, Q.23, Y.90, S.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.23, A:Y.90 SO4.13: 10 residues within 4Å: Chain B: G.16, G.17, Y.18, K.39, G.154, L.155, C.156, K.157 Ligands: STU.7, GOL.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.17, B:L.155 Water bridges: B:K.39, B:K.39, B:C.156, B:K.157 Salt bridges: B:K.39

1 x STU: STAUROSPORINE(Non-covalent)

STU.7: 24 residues within 4Å: Chain B: R.11, L.13, G.14, K.15, G.16, V.21, A.37, K.39, V.72, L.88, E.89, Y.90, L.91, S.92, G.94, E.95, M.98, E.138, N.139, M.141, T.151, F.153 Ligands: GOL.8, SO4.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.13, B:L.13, B:V.21, B:Y.90, B:E.95 Hydrogen bonds: B:E.89, B:L.91, B:E.138

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.14: 7 residues within 4Å: Chain B: D.73, E.89, N.143, H.144, Q.145, K.149, R.279 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.143, B:R.279 Salt bridges: B:E.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, J. et al., Development of Organometallic S6K1 Inhibitors. J.Med.Chem. (2015)

Release Date

2015-01-21

Peptides

Ribosomal protein S6 kinase beta-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosomal protein S6 kinase beta-1

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