SMTL ID : 7dsy.1

Crystal Structure of RNase L in complex with KM05073

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

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

25A.1: 22 residues within 4Å: Chain A: Q.17, E.38, 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 22 PLIP interactions: 15 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:S.48, A:Q.51, A:N.74, A:E.114, A:Y.118, A:G.150, B:R.292, B:Y.295, B:Y.295 Water bridges: A:K.72, A:K.72, A:D.105, A:N.107, B:W.337, B:I.348 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 25A.4: 20 residues within 4Å: Chain A: R.292, R.293, Y.295, R.338, F.347 Chain B: Q.17, W.41, W.43, S.48, Q.51, K.72, N.74, D.105, N.107, F.109, E.114, V.117, Y.118, R.138, G.150 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.17, B:S.48, B:Q.51, B:N.74, B:E.114, B:Y.118, B:Y.118, B:G.150, A:R.292, A:Y.295, A:Y.295 Salt bridges: B:K.72, B:R.138, A:R.338 pi-Stacking: B:W.43, B:W.43, B:W.43, B:F.109 pi-Cation interactions: A:R.292

2 x HFX: 1-chloranyl-3-methylsulfinyl-6,7-dihydro-5H-2-benzothiophen-4-one(Non-covalent)

HFX.2: 9 residues within 4Å: Chain A: W.326, I.354, A.355, L.417, C.420, Q.471, L.474, A.484, D.485 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.354, A:A.355 Water bridges: A:D.485 HFX.5: 11 residues within 4Å: Chain B: W.326, I.354, A.355, A.373, L.417, A.418, C.420, T.423, Q.471, L.474, D.485 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.354, B:A.355, B:L.474

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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