MolNFT v1 · #180342 · DNA

DNA-DB1879 complex: the DNA sequence 5'-cgcgaattcgcg-3' presents a binding site for the heterocyclic small molecule (DB1879).

7KWK · DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'): “DNA-DB1879 complex: the DNA sequence 5'-cgcgaattcgcg-3' presents a binding site for the heterocyclic small…”. X-ray diffraction, 2 ligands (X8V, MG), 1 pocket (best druggability…

PDB: 7KWK
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*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
Ligands: X8V, MG
Pockets: 1 · best druggability 0.25

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3')	dna	12	—	—

Ligands and binding sites

X8V · 2-[5-(4-carbamimidoylphenyl)thiophen-2-yl]-1H-indole-6-carboximidamide · ligand · chains A, B
MG · Magnesium ion · metal · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.25	0.73	13	X8V

Interfaces

1 interface between chains.

A–B · 558 Å² buried · 50 hydrogen bonds · nucleic-nucleic

Compared structures

7KWK · DNA-DB1879 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents a binding site for the… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7KWK · PDBe 7KWK

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