MolNFT v1 · #73328 · DNA

A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains

3NYP · 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3': “A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted…”. X-ray diffraction, 2 ligands (RNR, K), 1 pocket (best druggability 0.29).…

PDB: 3NYP
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
Ligands: RNR, K
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

RNR · 3,6-bis(3-(3'-(R)-fluoropyrrolindino)propionamido)acridine · ligand · chains A, B
K · Potassium ion · metal · 4 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	51	0.29	0.76	6	RNR

Interfaces

1 interface between chains.

A–B · 807 Å² buried · 37 hydrogen bonds · nucleic-nucleic

Compared structures

3NYP · A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with… · 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 3NYP · PDBe 3NYP

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