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MolNFT v1 · #45645 · DNA

An unexpected mode of small molecule DNA binding provides the structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin a

2N96 · DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3'): “An unexpected mode of small molecule DNA binding provides the structural basis for DNA cleavage by the potent…”. Solution nmr, 1 ligand (4JF), 1 pocket (best druggability 0.23). MolNFT v1…

PDB
2N96
Type
DNA
Length
16 nucleotides
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3')
Ligands
4JF
Pockets
1 · best druggability 0.23

Structure

solution nmr · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
X, YDNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3')dna8——

Ligands and binding sites

  • 4JF · (1R,1'R,2S,2'S,3R,3'R,5aR,10aR,11a'S)-2'-[(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)oxy]-2,2'-diethyl-11,11 '-dihydrazinyl-6,6',9,9'-tetrahydroxy-4,4',5,5',10,10'-hexaoxo-1,1'-bis{[2,4,6-trideoxy-4-(dimethylamino)-beta-L-arabino -hexopyranosyl]oxy}[2,2',3,3',4,4',5,5',5a,8,10,10',10a,11a'-tetradecahydro-1H,1'H-[3,3'-bibenzo[b]fluorene]]-2-yl 2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranoside · ligand · chains X, Y

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1500.230.728empty

Interfaces

1 interface between chains.

  • X–Y · 340 Ų buried · 28 hydrogen bonds · nucleic-nucleic

Compared structures

  • 2N96 · An unexpected mode of small molecule DNA binding provides the structural basis for DNA… · the same entry in another collection · chain X against X, TM-score 1.00

Analyse

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