NMR Ensemble

1CP8

NMR STRUCTURE OF DNA (5'-D(TTGGCCAA)2-3') COMPLEXED WITH NOVEL ANTITUMOR DRUG UCH9

Structural Biology Knowledgebase: 1CP8 SBKB.org


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: --
  • Conformers Submitted: 1
  • Selection Criteria: Least Restraint Violation

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1CP8

Classification: DNA

Total Structure Weight: 7140.12

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*TP*TP*GP*GP*CP*CP*AP*A)-3') A, B 8 synthetic TWO MOLECULES OF THE DRUG UCH9 (DDA-DXA-DDA-DDL-DRI-DDA) BOUND IN THE MINOR GROOVE THE MODEL CONTAINS TWO MOLECULES OF UCH9 AND ONE MG CATION WHICH IS COORDINATED TO TWO UCH9 MOLECULES. IN THIS ENTRY UCH9 IS PRESENTED AS HET GROUP, DDA-DXA-DDA-DDL-DRI-DDA. THESE GROUPS ARE NUMBERED 1-6 FOR ONE UCH9 AND 7-12 FOR THE OTHER UCH9.

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DXA
Query on DXA

A, B 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2- OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYDROXY-7- (SEC-BUTYL)-ANTHRACENE
C24 H30 O7
XGORHSPGULYMCV-HHYQQTLHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DRI
Query on DRI

A, B 4-O-METHYL-2,6-DIDEOXY-BETA-D-GLUCOSE
4-O-METHYL-2,6-DIDEOXY-BETA-D-MANNOSE (Synonym)
C7 H14 O4
CDRBUGSWTNDUSM-DBRKOABJSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DDA
Query on DDA

A, B 2,6-DIDEOXY-BETA-D-GLUCOSE
2,6-DIDEOXY-BETA-D-MANNOSE (Synonym)
C6 H12 O4
FDWRIIDFYSUTDP-KVTDHHQDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DDL
Query on DDL

A, B 2,6-DIDEOXY-BETA-D-GALACTOSE
2,6-DIDEOXY-BETA-D-TALOSE (Synonym)
C6 H12 O4
FDWRIIDFYSUTDP-KAZBKCHUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: --
  • Conformers Submitted: 1
  • Selection Criteria: LEAST RESTRAINT VIOLATION

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1999-06-11
  • Released Date: 1999-07-01
  • Deposition author(s): Katahira, R., Katahira, M., Yamashita, Y., Ogawa, H., Kyogoku, Y., Yoshida, M.

Revision History

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