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NMR structure of the parallel-stranded DNA quadruplex D(TTAGGGT)4 complexed with the telomerase inhibitor RHPS4

Analyse NMR structure of the parallel-stranded DNA quadruplex D(TTAGGGT)4 complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1NZM
Type
DNA
Length
28 nucleotides
Chains
4
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*TP*TP*AP*GP*GP*GP*T)-3'
Ligands
LG1, K
Pockets
2 · best druggability 0.44

Structure

solution nmr · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D5'-D(*TP*TP*AP*GP*GP*GP*T)-3'dna7——

Ligands and binding sites

  • LG1 · 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridin-13-ium · ligand · 2 copies · chains A, B, C, D
  • K · Potassium ion · metal · 2 copies · chains A, B, C, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11550.440.769LG1
2800.320.748LG1

Interfaces

6 interfaces between chains.

  • B–C · 353 Ų buried · 18 hydrogen bonds · nucleic-nucleic
  • C–D · 320 Ų buried · 16 hydrogen bonds · nucleic-nucleic
  • A–B · 285 Ų buried · 14 hydrogen bonds · nucleic-nucleic
  • A–D · 255 Ų buried · 13 hydrogen bonds · nucleic-nucleic
  • A–C · 145 Ų buried · 3 hydrogen bonds · nucleic-nucleic

Compared structures

  • 1NZM · NMR structure of the parallel-stranded DNA quadruplex d(TTAGGGT)4 complexed with the… · the same entry in another collection · chain B against B, TM-score 1.00

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