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A bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule BRACO19

Analyse A bimolecular parallel-stranded human telomeric quadruplex in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CE5
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
Ligands: BRA, K
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

BRA · 9-[4-(n,n-dimethylamino)phenylamino]-3,6-bis(3-pyrrolidinopropionamido) acridine · ligand · chains A, B
K · Potassium ion · metal · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	70	0.31	0.75	8	empty

Interfaces

1 interface between chains.

A–B · 441 Å² buried · 25 hydrogen bonds · nucleic-nucleic

Compared structures

3CE5 · A bimolecular parallel-stranded human telomeric quadruplex in complex with a… · 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 3CE5 · PDBe 3CE5

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