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MolNFT v1 · #144910 · RNA

RNA-imidazolium-bridged intermediate complex, 4H soaking

6C8E · RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)…: “RNA-imidazolium-bridged intermediate complex, 4H soaking”. X-ray diffraction, 1 ligand (EQ1), 1 pocket (best druggability 0.51). MolNFT v1 #144910 on GenesisL1: 3D structure, binding sites…

PDB
6C8E
Type
RNA
Length
28 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
Ligands
EQ1
Pockets
1 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')rna14——

Ligands and binding sites

  • EQ1 · [2-azanyl-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-1-yl]-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methoxy]phosphinic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13680.510.7322empty

Interfaces

1 interface between chains.

  • A–B · 594 Ų buried · 53 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 modified (nucleotide modification).

Compared structures

  • 6C8E · RNA-imidazolium-bridged intermediate complex, 4h soaking · the same entry in another collection · chain A against A, TM-score 1.00

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