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Compound: DAE
Formula: C8 H10 BE F3 N3 O11 P2 1-
Name(s):
  • o,p-dinitrophenyl aminoethyldiphosphate-beryllium trifluoride
Experimental: PDB entry 1d1a | Residue 999 | Resolution 2.00 Å | MSD | RCSB | EDS | PDBsum | PDBREPORT | OCA | JenaLib | MMDB

Coordinates
PDB file (".pdb"; experimental coordinates for 28 atoms from PDB entry 1d1a)
PDB file (".txt"; experimental coordinates)
No ideal coordinates available for this compound (MSDchem file with too many short distances for DAE)
Clean PDB file (".pdb"; no REMARKs; ATOM records; experimental coordinates; used for generating all derived data and dictionaries)
Clean PDB file (".txt"; no REMARKs; ATOM records; experimental coordinates; used for generating all derived data and dictionaries)

Visualisation
Jmol page
ChemScape Chime page
VRML file (gzip-ed)

Dictionaries
PDB dictionary file (CONECT records, etc.)
X-PLOR/CNS topology file
X-PLOR/CNS parameter file (1 warnings, 0 notes)
X-PLOR/CNS energy minimisation input file
O dictionary entry (add to the .bonds_angles datablock)
O RS_FIT datablock (not needed in O 9.0 or later)
O RSR datablock (not needed in O 9.0 or later)
O connectivity entry (not needed in O 9.0 or later)
O torsion entry (not needed in O 9.0 or later; NOTE: depending on the version of O that you use, you may need to remove the target values of the angles)
TNT dictionary file

Miscellaneous
Disclaimer
EDS statistics
HETZE log file (rudimentary quality assessment)
Connection table file
No superstructures found

Off-site
Action!
What?
Where?
Hit the link or button to visit the site or server
Description of what the site or server does or contains
Name and location of the site or server (links can be found in the main HIC-Up menu)
Validation
Compare all instances of "DAE" in the PDB to the ideal structure ValLigURL (Uppsala University)
Go! View model and electron density for "DAE 999" in PDB entry 1d1a (opens Java viewer) EDS (Uppsala University)
Go! Main EDS page for parent PDB entry 1d1a EDS (Uppsala University)
Description
Generate hydrogens and dictionaries (MDL, GROMOS87, GROMACS, REFMAC5, SYBYL2, AUTODOCK, WHAT IF, HEX, CNS, O, and SHELX) for "DAE" using the clean PDB file as input PRODRG2 server (University of Dundee)
Go! Ligand chemistry for "DAE" in MSDchem MSD (EBI)
Go! Ligand chemistry for "DAE" from MSDchem in XML format MSD (EBI)
Go! Information about "DAE" in ChEBI ChEBI (EBI)
Run Babel to convert the clean PDB file of "DAE" to canonical SMILES and other formats ChemDB (UC Irvine)
Go! Ligand chemistry for DAE in MSDchem@RCSB MSDchem@RCSB (Rutgers)
Go! CIF dictionary for "DAE" Ligand Depot (Rutgers)
PDB entries
Go! List of all PDB entries containing "DAE" from MSDmotif MSD (EBI)
Go! List of unique PDB entries containing "DAE" from MSDmotif MSD (EBI)
Go! Download all instances of "DAE" in the PDB including their environment (tar-file) MSD (EBI)
Go! List of PDB entries containing "DAE" PDBsum (EBI)
Go! List of PDB entries containing "DAE" RCSB
Go! List of PDB entries containing "DAE" Ligand Depot (Rutgers)
Go! List of PDB entries containing "DAE" DHC JenaLib (Fritz Lipmann Institute)
Go! List of PDB entries containing "DAE" OCA (Weizmann Institute)
Structural biology
Go! List PDB entries for which "DAE" is a cognate ligand PROCOGNATE (EBI)
Go! Statistics about protein residues that interact with "DAE" from MSDmotif MSD (EBI)
Go! Statistics about nucleic acid residues that interact with "DAE" from MSDmotif MSD (EBI)
Go! Statistics about other ligands that interact with "DAE" from MSDmotif MSD (EBI)
Go! Statistics about PROSITE motifs that interact with "DAE" from MSDmotif MSD (EBI)
Go! Statistics about small 3D motifs that interact with "DAE" from MSDmotif MSD (EBI)
Go! Statistics about secondary structure elements that interact with "DAE" from MSDmotif MSD (EBI)
Search for "DAE" in ReliBase ReliBase (CCDC)
Go! List of PDB entries containing "DAE" and interacting residues FireDB (Spain)
Go! Search for "DAE" in the PDB-Ligand database PDB-Ligand (Korea)
Miscellaneous
Go! Search for "DAE" in the PubChem compound database PubChem (NCBI)
Go! Search for "C8 H10 BE F3 N3 O11 P2 1-" in the Chemistry Webbook Chemistry Webbook (NIST)
Search for "o,p-dinitrophenyl aminoethyldiphosphate-beryllium trifluoride" in the ChemDB compound database ChemDB (UC Irvine)
Go! Search for "o,p-dinitrophenyl aminoethyldiphosphate-beryllium trifluoride" in the KEGG-Ligand database KEGG-Ligand (Kyoto University)
Go! Search for "o,p-dinitrophenyl aminoethyldiphosphate-beryllium trifluoride" with Google Google

Summary of HETZE report :

 Residue type                   : (DAE) 
 Identifier                     : ( 2861) 
 Segment ID                     : ( ) 

 Nr of atoms                    : (      28) 
 List of elements (from file)   : ( C8 H10 BE F3 N3 O11 P2 1-) 
 Deduced formula                : (BE1 C8 N3 O11 F3 P2) 
 Guestimated total nr of Hs     : (      17) 
 Nr of extra examples           : (       0) 

 Nr of distances < 0.8 A        : (       0) 
 Nr of bond angles < 80 degrees : (       0) 

 Nr of bonds found              : (      27) 
 ... bonds without ideal value  : (       3) 
 ... bonds near ideal value     : (      16) 
 ... bonds far from ideal value : (       8) 
          -"-                 % : (  29.630) 

 Nr of angles found             : (      38) 

 Nr of dihedrals found          : (      35) 

 Nr of atoms with impropers     : (       8) 
 ... imprs far from ideal value : (       0) 
          -"-                 % : (   0.000) 

 Nr of flat planes              : (       7) 


2D structure diagram from MSDchem

2D structure diagram from MSDchem@RCSB

3D Image generated with LIGPLOT

RASMOL image provided by Barani


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This page was created on Fri Feb 29 11:38:56 2008.