SMTL ID : 7dts.1

Crystal structure of RNase L in complex with AC40357

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

homo-dimer

Ligands

2 x 25A: 5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE(Non-covalent)(Covalent)

25A.1: 21 residues within 4Å: Chain A: Q.17, W.41, W.43, S.48, Q.51, K.72, N.74, I.84, D.105, N.107, F.109, E.114, V.117, Y.118, R.138, G.150 Chain B: R.292, R.293, Y.295, R.338, F.347 17 PLIP interactions: 5 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:R.292, B:Y.295, B:Y.295, A:Q.51, A:Q.51, A:N.74, A:E.114, A:Y.118, A:Y.118 Salt bridges: B:R.338, A:K.72, A:R.138 pi-Cation interactions: B:R.292 Water bridges: A:Y.191 pi-Stacking: A:W.43, A:W.43, A:F.109 25A.4: 18 residues within 4Å: Chain A: R.292, R.293, Y.295, R.338, F.347 Chain B: E.38, W.41, W.43, S.48, Q.51, K.72, N.74, D.105, N.107, F.109, E.114, Y.118, K.149 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.48, B:Q.51, B:N.74, B:N.107, B:E.114, B:Y.118, B:Y.118, B:K.149, B:K.149, A:R.292, A:R.292, A:Y.295, A:Y.295 Water bridges: B:Y.191 Salt bridges: B:K.72, B:R.138, B:K.149, A:R.338 pi-Stacking: B:W.43, B:W.43, B:F.109, B:F.109 pi-Cation interactions: A:R.292

2 x 27K: butyl 4-hydroxybenzoate(Non-covalent)

27K.2: 15 residues within 4Å: Chain A: R.325, I.362, A.373, K.375, L.417, A.418, L.419, C.420, E.421, Y.422, T.423, E.426, L.474, A.484, D.485 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.362, A:A.373, A:L.417, A:L.474, A:A.484 Hydrogen bonds: A:C.420, A:D.485 27K.5: 16 residues within 4Å: Chain B: R.325, W.326, I.354, I.362, A.373, L.417, A.418, L.419, C.420, E.421, Y.422, T.423, E.426, L.474, A.484, D.485 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.326, B:I.354, B:I.362, B:A.373, B:L.417, B:L.474 Hydrogen bonds: B:C.420, B:D.485 Water bridges: B:E.387

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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