MolNFT v1 · #41984 · DNA

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.

2K4L · 5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*D…: “Solution structure of a 2:1C2-(2-NAPHTHYL)PYRROLO[2,1-C][1, 4]BENZODIAZEPINE (pbd) DNA adduct: molecular…”. Solution nmr, 1 ligand (PZD), 1 pocket (best druggability…

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.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(DAPDAPDTPDCPDTPDTPDTPDAPDAPDAPDGPDAPDTPD T)-3'	dna	14	—	—

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	142	0.42	0.75	18	PZD

Interfaces

1 interface between chains.

A–B · 654 Å² 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

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2K4L · PDBe 2K4L

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