SMTL ID : 2wpu.1

Chaperoned ruthenium metallodrugs that recognize telomeric DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-tetramer

Ligands

4 x KYT: (3AS,4S,6AR)-4-(5-((3R,4R)-3,4-DIAMINOPYRROLIDIN-1-YL)-5-OXOPENTYL)TETRAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-2(3H)-ONE-P-CYMENE-CHLORO-RUTHENIUM(III)(Non-covalent)

KYT.1: 21 residues within 4Å: Chain A: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, K.121, D.128 Chain B: W.120 Ligands: GOL.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.79, A:W.79, A:L.110, A:T.114 Hydrogen bonds: A:N.23, A:S.27, A:Y.43, A:S.45, A:N.49, A:S.112, A:S.112, A:D.128 KYT.4: 21 residues within 4Å: Chain A: W.120 Chain B: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, K.121, D.128 Ligands: GOL.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.79, B:W.79, B:L.110, B:T.114 Hydrogen bonds: B:N.23, B:S.27, B:Y.43, B:S.45, B:N.49, B:S.112, B:S.112, B:D.128 KYT.7: 21 residues within 4Å: Chain C: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, K.121, D.128 Chain D: W.120 Ligands: GOL.9 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.79, C:W.79, C:L.110, C:T.114 Hydrogen bonds: C:N.23, C:S.27, C:S.45, C:N.49, C:S.112, C:S.112, C:D.128 KYT.10: 21 residues within 4Å: Chain C: W.120 Chain D: N.23, L.25, S.27, Y.43, S.45, V.47, G.48, N.49, W.79, A.86, S.88, T.90, W.92, W.108, L.110, S.112, T.114, K.121, D.128 Ligands: GOL.12 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.79, D:W.79, D:L.110, D:T.114 Hydrogen bonds: D:N.23, D:S.27, D:S.45, D:N.49, D:S.112, D:S.112, D:D.128

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

SO4.2: 2 residues within 4Å: Chain A: H.87 Chain C: A.65 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.85, A:N.85, A:H.87, A:H.87 Salt bridges: A:H.87 SO4.5: 2 residues within 4Å: Chain B: H.87 Chain D: A.65 5 PLIP interactions: 5 interactions with chain B Water bridges: B:N.85, B:N.85, B:H.87, B:H.87 Salt bridges: B:H.87 SO4.8: 2 residues within 4Å: Chain A: A.65 Chain C: H.87 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Water bridges: C:N.85, C:N.85, C:H.87, A:A.63 Salt bridges: C:H.87 SO4.11: 2 residues within 4Å: Chain B: A.65 Chain D: H.87 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Water bridges: D:N.85, D:N.85, D:H.87, B:A.63 Salt bridges: D:H.87

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: N.49 Chain B: K.121 Ligands: KYT.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.49 GOL.6: 3 residues within 4Å: Chain A: K.121 Chain B: N.49 Ligands: KYT.4 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.49 GOL.9: 3 residues within 4Å: Chain C: N.49 Chain D: K.121 Ligands: KYT.7 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.49 GOL.12: 3 residues within 4Å: Chain C: K.121 Chain D: N.49 Ligands: KYT.10 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimbron, J.M. et al., Chemo-Genetic Optimization of DNA Recognition by Metallodrugs Using a Presenter-Protein Strategy. Chemistry (2010)

Release Date

2010-10-13

Peptides

STREPTAVIDIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

STREPTAVIDIN

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