1P96

Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA

Structural Biology Knowledgebase: 1P96 SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10
  • Conformers Submitted: 10
  • Selection Criteria: All Calculated Structures Submitted

Literature

Macromolecules
Sequence Display for 1P96

Classification: DNA

Total Structure Weight: 8489.84

Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3' A 14 synthetic
5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3' B 12 synthetic

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

A SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2- B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO- 2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A- HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI)
C31 H31 N O7
QJIOPAVNMIETIF-DERWUGRYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DDI N/A in BindingDB
N/A in BindingMoad
Kd: 2540 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10
  • Conformers Submitted: 10
  • Selection Criteria: all calculated structures submitted

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2003-05-09
  • Released Date: 2003-08-26
  • Deposition author(s): Hwang, G.S., Jones, G.B., Goldberg, I.H.

Revision History

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