MolNFT v1 · #150064 · DNA

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)

6GIM · DNA (5'-D(*AP*AP*AP*TP*TP*T)-3'): “Structure of the DNA duplex D(AAATTT)2 with [N-(3-chloro-4-((4,5…”. X-ray diffraction, 2 ligands (EZK, MG). MolNFT v1 #150064 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GIM
Type: DNA
Length: 24 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
Ligands: EZK, MG

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, A, B	DNA (5'-D(APAPAPTPTPT)-3')	dna	6	—	—

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 Å² buried · 19 hydrogen bonds · nucleic-nucleic
D–A · 131 Å² buried · 2 hydrogen bonds · nucleic-nucleic
C–A · 94 Å² buried · 3 hydrogen bonds · nucleic-nucleic
C–B · 59 Å² buried · 2 hydrogen bonds · nucleic-nucleic
D–B · 15 Å² 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

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