MolNFT v1 · #29982 · DNA

Crystal structure analysis of the minor groove binding quinolinium quaternary salt sn 8315 complexed with cgcgaattcgcg

1ZPH · 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3': “Crystal structure analysis of the minor groove binding quinolinium quaternary salt sn 8315 complexed with…”. X-ray diffraction, 2 ligands (SN8, MG), 1 pocket (best druggability 0.25).…

PDB: 1ZPH
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
Ligands: SN8, MG
Pockets: 1 · best druggability 0.25

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

SN8 · 1,6-dimethyl-4-(4-(4-(1-methylpyridinium-4-ylamino)phenylcarbamoyl)phenylamino)quinolinium · 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	57	0.25	0.73	13	SN8

Interfaces

1 interface between chains.

A–B · 564 Å² buried · 54 hydrogen bonds · nucleic-nucleic

Compared structures

1ZPH · Crystal structure analysis of the minor groove binding quinolinium quaternary salt SN… · 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 1ZPH · PDBe 1ZPH

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