2K4L

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.

Structural Biology Knowledgebase: 2K4L SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200
  • Conformers Submitted: 10
  • Selection Criteria: Structures with the Lowest Energy

Literature

Macromolecules
Sequence Display for 2K4L

Classification: DNA

Total Structure Weight: 9328.62

Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*DT)-3' A, B 14 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PZD
Query on PZD

A, B (11aS)-7,8-dimethoxy-2-naphthalen-2-yl-1,10,11,11a- tetrahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin- 5-one
C24 H22 N2 O3
QCHVNYAXOGUSSL-IBGZPJMESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200
  • Conformers Submitted: 10
  • Selection Criteria: structures with the lowest energy

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2008-06-13
  • Released Date: 2008-10-28
  • Deposition author(s): Antonow, D., Barata, T., Jenkins, T.C., Parkinson, G.N., Howard, P.W., Thurston, D.E., Zloh, M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4