1DSI

Solution structure of a duocarmycin sa-indole-alkylated dna dupleX

• PDB DOI: https://doi.org/10.2210/pdb1DSI/pdb
• NAKB: 1DSI

• Classification: DNA
• Mutation(s): No 


• Deposited: 1998-07-29 Released: 1998-08-05 
• Deposition Author(s): Schnell, J.R., Ketchem, R.R., Boger, D.L., Chazin, W.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 20 
• Selection Criteria: LOWEST RESTRAINT VIOLATIONS 

Literature

Binding-Induced Activation of DNA Alkylation by Duocarmycin SA: Insights from the Structure of an Indole Derivative-DNA Adduct

Schnell, J.R., Ketchem, R.R., Boger, D.L., Chazin, W.J.

(1999) J Am Chem Soc 121: 5645-5652

• DOI: https://doi.org/10.1021/ja983556j

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.09 kDa 
• Atom Count: 474 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3')	A	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3')	B	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DSI	C [auth B]	4-HYDROXY-6-(1H-INDOLE-2-CARBONYL)-8-METHYL-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER C22 H19 N3 O4 SVXVQSGKGYZESS-LLVKDONJSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 20 
• Selection Criteria: LOWEST RESTRAINT VIOLATIONS 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-08-05 
Deposition Author(s): Schnell, J.R., Ketchem, R.R., Boger, D.L., Chazin, W.J.

Revision History  

• Version 1.0: 1998-08-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection