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Solution structure of a covalently bound PYRROLO[2,1-C][1, 4]BENZODIAZEPINE-benzimidazole hybrid to a 10MER DNA duplex

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

PDB: 2KTT
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'
Ligands: PBH
Pockets: 1 · best druggability 0.30

Structure

solution nmr · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(APAPCPAPAPTPTPGPTPT)-3'	dna	10	—	—

Ligands and binding sites

PBH · (11aS)-7-methoxy-8-(3-{4-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]phenoxy}propoxy)-1,2,3,10,11,11a-hexahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one · ligand · 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	67	0.30	0.74	12	PBH

Interfaces

1 interface between chains.

A–B · 435 Å² buried · 34 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

2KTT · Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole… · the same entry in another collection · chain A against A, TM-score 1.00

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

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