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Solution structure of a 2:1C2-(2-NAPHTHYL)PYRROLO[2,1-C][1, 4]BENZODIAZEPINE (pbd) DNA adduct: molecular basis for unexpectedly high DNA helix stabilization.

Analyse Solution structure of a 2:1C2-(2-NAPHTHYL)PYRROLO[2,1-C][1, 4]BENZODIAZEPINE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2K4L
Type
DNA
Length
28 nucleotides
Chains
2
Method
solution nmr
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*D T)-3'
Ligands
PZD
Pockets
1 · best druggability 0.42

Structure

solution nmr · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*D T)-3'dna14——

Ligands and binding sites

  • PZD · (11aS)-7,8-dimethoxy-2-naphthalen-2-yl-1,10,11,11a-tetrahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one · ligand · 2 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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11420.420.7518PZD

Interfaces

1 interface between chains.

  • A–B · 654 Ų buried · 58 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

  • 2K4L · Solution structure of a 2:1C2-(2-naphthyl)pyrrolo[2,1-c][1,4]benzodiazepine (PBD) DNA… · the same entry in another collection · chain A against A, TM-score 1.00

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