Research workbench

A 2:1 stoichiometric complex of anticancer drug adriamycin bound to parallel G-quadruplex DNA [D-(TTGGGGT)]4.

Analyse A 2:1 stoichiometric complex of anticancer drug adriamycin bound to parallel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CSK
Type: DNA
Length: 28 nucleotides
Chains: 4
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*TP*TP*GP*GP*GP*GP*T)-3')
Ligands: DM2
Pockets: 1 · best druggability 0.34

Structure

solution nmr · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D(TPTPGPGPGPGP*T)-3')	dna	7	—	—

Ligands and binding sites

DM2 · Doxorubicin · ligand · 2 copies · chains A, D, 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	60	0.34	0.78	6	empty

Interfaces

6 interfaces between chains.

B–C · 462 Å² buried · 18 hydrogen bonds · nucleic-nucleic
A–B · 378 Å² buried · 18 hydrogen bonds · nucleic-nucleic
A–D · 337 Å² buried · 17 hydrogen bonds · nucleic-nucleic
C–D · 310 Å² buried · 15 hydrogen bonds · nucleic-nucleic
B–D · 227 Å² buried · 9 hydrogen bonds · nucleic-nucleic

Compared structures

7CSK · A 2:1 stoichiometric complex of anticancer drug Adriamycin bound to parallel G-quadruplex… · 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 7CSK · PDBe 7CSK

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.