SMTL ID : 7elw.1

Crystal structure of RNase L in complex with Myricetin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.55 Å

Oligo State

homo-dimer

Ligands

2 x 25L: [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

25L.1: 18 residues within 4Å: Chain A: W.41, W.43, S.48, Q.51, K.72, N.74, I.84, D.105, N.107, F.109, E.114, Y.118, R.138 Chain B: R.292, R.293, Y.295, R.338, F.347 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:W.43, A:S.48, A:Q.51, A:N.74, A:N.107, A:E.114, A:Y.118, B:R.292, B:Y.295 Salt bridges: A:K.72, A:R.138, B:R.338 pi-Stacking: A:W.43, A:W.43, A:F.109 pi-Cation interactions: B:R.292, B:R.292 25L.4: 17 residues within 4Å: Chain A: R.292, Y.295, R.338, F.347 Chain B: W.41, W.43, S.48, Q.51, K.72, N.74, D.105, N.107, F.109, E.114, Y.118, R.138, G.150 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:W.43, B:S.48, B:Q.51, B:N.107, B:E.114, B:Y.118, B:Y.118, B:G.150, A:R.292, A:Y.295 Salt bridges: B:K.72, B:R.138, A:R.338 pi-Stacking: B:W.43, B:W.43, B:F.109 pi-Cation interactions: A:R.292, A:R.292

2 x MYC: 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE(Non-covalent)

MYC.2: 14 residues within 4Å: Chain A: R.325, I.354, A.355, I.362, A.373, L.417, A.418, L.419, C.420, T.423, E.426, L.474, A.484, D.485 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.354, A:A.355, A:I.362, A:A.373, A:L.417 Hydrogen bonds: A:R.325, A:R.325, A:C.420, A:C.420, A:T.423, A:E.426, A:D.485 MYC.5: 16 residues within 4Å: Chain B: R.325, I.354, A.355, I.362, A.373, K.375, V.401, L.417, A.418, L.419, C.420, T.423, E.426, L.474, A.484, D.485 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.354, B:I.362, B:A.373, B:L.417, B:A.484 Hydrogen bonds: B:R.325, B:R.325, B:C.420, B:C.420, B:E.421, B:T.423, B:E.426, B:D.485, B:D.485

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

PO4.3: 4 residues within 4Å: Chain A: R.660, H.665 Chain B: R.660, H.665 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.660, A:H.665, B:R.660, B:H.665

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, J. et al., Identification of Small Molecule Inhibitors of RNase L by Fragment-Based Drug Discovery. J.Med.Chem. (2022)

Release Date

2021-11-24

Peptides

Ribonuclease L: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

Ribonuclease L

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