Structure of the DNA duplex D(AAATTT)2 with [N-(3-chloro-4-((4,5- dihydro-1H-imidazol-2-YL)AMINO)PHENYL)-4-((4,5-dihydro-1H-imidazol-2- YL)AMINO)BENZAMIDE] - (drug JNI18)

Structure

x-ray diffraction · 1 distinct chain.

Ligands and binding sites

• EZK · [4-[(3-chloranyl-4-imidazolidin-2-ylideneazaniumyl-phenyl)carbamoyl]phenyl]-imidazolidin-2-ylidene-azanium · ligand · 3 copies · chains D, C, A, B
• MG · Magnesium ion · metal · 3 copies · chains C, A, B

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

Interfaces

5 interfaces between chains.

• A–B · 250 Ų buried · 19 hydrogen bonds · nucleic-nucleic
• D–A · 131 Ų buried · 2 hydrogen bonds · nucleic-nucleic
• C–A · 94 Ų buried · 3 hydrogen bonds · nucleic-nucleic
• C–B · 59 Ų buried · 2 hydrogen bonds · nucleic-nucleic
• D–B · 15 Ų buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

• 6GIM · Structure of the DNA duplex d(AAATTT)2 with [N-(3-chloro-4-((4,5-dihydro-1H-imidazol-2-yl)… · the same entry in another collection · chain D against D, 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 6GIM · PDBe 6GIM