SMTL ID : 6m13.1

Crystal structure of Rnase L in complex with Toceranib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-dimer

Ligands

2 x BWC: 5-[(Z)-(5-fluoranyl-2-oxidanylidene-1H-indol-3-ylidene)methyl]-2,4-dimethyl-N-(2-pyrrolidin-1-ylethyl)-1H-pyrrole-3-carboxamide(Non-covalent)

BWC.1: 12 residues within 4Å: Chain A: I.354, A.355, A.373, L.417, A.418, L.419, C.420, T.423, E.426, Q.471, L.474, D.485 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.354, A:A.355, A:A.373, A:L.417, A:Q.471, A:L.474, A:L.474, A:L.474 Hydrogen bonds: A:I.354, A:T.423, A:Q.471, A:D.485 Salt bridges: A:E.426 BWC.4: 13 residues within 4Å: Chain B: I.354, A.355, I.362, A.373, L.417, A.418, L.419, C.420, T.423, E.426, Q.471, L.474, D.485 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.355, B:A.373, B:L.417, B:L.474, B:L.474, B:L.474 Hydrogen bonds: B:I.354, B:D.485

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.2: 20 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 Chain B: R.292, R.293, Y.295, R.338, F.347 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.17, A:W.43, A:Q.51, A:Q.51, A:N.74, 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 25L.5: 19 residues within 4Å: Chain A: R.292, R.293, 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, K.149, G.150 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.51, B:Q.51, B:E.114, B:Y.118, B:Y.118, B:G.150, A:R.292, A:Y.295, A:R.338 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

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

PO4.3: 5 residues within 4Å: Chain A: R.660, E.664, H.665 Chain B: R.660, H.665 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.660, B:H.665, A:R.660, A:H.665

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, J. et al., Sunitinib inhibits RNase L by destabilizing its active dimer conformation. Biochem.J. (2020)

Release Date

2020-09-02

Peptides

Ribonuclease L: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

Ribonuclease L

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