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MolNFT v1 · #85009 · DNA

DNA minor-groove recognition of a tris-benzimidazole drug

459D · DNA (5'-D(*CP*GP*(CBR) P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3'): “DNA minor-groove recognition of a tris-benzimidazole drug”. X-ray diffraction, 1 ligand (TBZ), 1 pocket (best druggability 0.25). MolNFT v1 #85009 on GenesisL1: 3D structure…

PDB
459D
Type
DNA
Length
24 nucleotides
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (5'-D(*CP*GP*(CBR) P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3'); DNA…
Ligands
TBZ
Pockets
1 · best druggability 0.25

Structure

x-ray diffraction · 2 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (5'-D(*CP*GP*(CBR) P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3')dna12——
BDNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*AP*TP*GP*CP*G)- 3')dna12——

Ligands and binding sites

  • TBZ · 2''-(4-methoxyphenyl)-5-(3-amino-1-pyrrolidinyl)-2,5',2',5''-tri-benzimidazole · ligand · 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, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1530.250.7313TBZ

Interfaces

1 interface between chains.

  • A–B · 558 Ų buried · 58 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

  • 459D · DNA minor-groove recognition of a tris-benzimidazole drug · the same entry in another collection · chain A against A, TM-score 1.00

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