HIC-Up files for compound ADS adenosine-5p-(dithio)phosphate

Compound:	ADS
Formula:	C10 H14 N5 O5 P S2
Name(s):	adenosine-5p-(dithio)phosphate
Experimental:	PDB entry 1ak0 \| Residue 292 \| Resolution 1.80 Å \| MSD \| RCSB \| PDBsum \| PDBREPORT \| OCA \| JenaLib \| MMDB

Coordinates

PDB file (".pdb"; ideal coordinates for 23 atoms from MSDchem)

PDB file (".pdb"; experimental coordinates for 18 atoms from PDB entry 1ak0)

PDB file (".txt"; ideal coordinates)

PDB file (".txt"; experimental coordinates)

WARNING - Different number of atoms in the files with experimental and ideal coordinates!

Clean PDB file (".pdb"; no REMARKs; ATOM records; ideal coordinates; used for generating all derived data and dictionaries)

Clean PDB file (".txt"; no REMARKs; ATOM records; ideal 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 (0 warnings, 1 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

No EDS statistics available for this compound

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 "ADS" in the PDB to the ideal structure	ValLigURL (Uppsala University)
Description
	Generate hydrogens and dictionaries (MDL, GROMOS87, GROMACS, REFMAC5, SYBYL2, AUTODOCK, WHAT IF, HEX, CNS, O, and SHELX) for "ADS" using the clean PDB file as input	PRODRG2 server (University of Dundee)
Go!	Ligand chemistry for "ADS" in MSDchem	MSD (EBI)
Go!	Ligand chemistry for "ADS" from MSDchem in XML format	MSD (EBI)
Go!	Information about "ADS" in ChEBI	ChEBI (EBI)
	Run Babel to convert the clean PDB file of "ADS" to canonical SMILES and other formats	ChemDB (UC Irvine)
Go!	Ligand chemistry for ADS in MSDchem@RCSB	MSDchem@RCSB (Rutgers)
Go!	CIF dictionary for "ADS"	Ligand Depot (Rutgers)
PDB entries
Go!	List of all PDB entries containing "ADS" from MSDmotif	MSD (EBI)
Go!	List of unique PDB entries containing "ADS" from MSDmotif	MSD (EBI)
Go!	Download all instances of "ADS" in the PDB including their environment (tar-file)	MSD (EBI)
Go!	List of PDB entries containing "ADS"	PDBsum (EBI)
Go!	List of PDB entries containing "ADS"	RCSB
Go!	List of PDB entries containing "ADS"	Ligand Depot (Rutgers)
Go!	List of PDB entries containing "ADS"	DHC JenaLib (Fritz Lipmann Institute)
Go!	List of PDB entries containing "ADS"	OCA (Weizmann Institute)
Structural biology
Go!	List PDB entries for which "ADS" is a cognate ligand	PROCOGNATE (EBI)
Go!	Statistics about protein residues that interact with "ADS" from MSDmotif	MSD (EBI)
Go!	Statistics about nucleic acid residues that interact with "ADS" from MSDmotif	MSD (EBI)
Go!	Statistics about other ligands that interact with "ADS" from MSDmotif	MSD (EBI)
Go!	Statistics about PROSITE motifs that interact with "ADS" from MSDmotif	MSD (EBI)
Go!	Statistics about small 3D motifs that interact with "ADS" from MSDmotif	MSD (EBI)
Go!	Statistics about secondary structure elements that interact with "ADS" from MSDmotif	MSD (EBI)
	Search for "ADS" in ReliBase	ReliBase (CCDC)
Go!	List of PDB entries containing "ADS" and interacting residues	FireDB (Spain)
Go!	Search for "ADS" in the PDB-Ligand database	PDB-Ligand (Korea)
Miscellaneous
Go!	Search for "ADS" in the PubChem compound database	PubChem (NCBI)
Go!	Search for "C10 H14 N5 O5 P S2" in the Chemistry Webbook	Chemistry Webbook (NIST)
	Search for "adenosine-5p-(dithio)phosphate" in the ChemDB compound database	ChemDB (UC Irvine)
Go!	Search for "adenosine-5p-(dithio)phosphate" in the KEGG-Ligand database	KEGG-Ligand (Kyoto University)
Go!	Search for "adenosine-5p-(dithio)phosphate" with Google	Google

Summary of HETZE report :

 Residue type                   : (ADS) 
 Identifier                     : ( 1454) 
 Segment ID                     : ( ) 

 Nr of atoms                    : (      23) 
 List of elements (from file)   : ( C10 H14 N5 O5 P S2) 
 Deduced formula                : (C10 N5 O5 P1 S2) 
 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              : (      25) 
 ... bonds without ideal value  : (       2) 
 ... bonds near ideal value     : (      22) 
 ... bonds far from ideal value : (       1) 
          -"-                 % : (   4.000) 

 Nr of angles found             : (      38) 

 Nr of dihedrals found          : (      49) 

 Nr of atoms with impropers     : (       9) 
 ... imprs far from ideal value : (       0) 
          -"-                 % : (   0.000) 

 Nr of flat planes              : (       4)

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HIC-Up release 12.1 [2008-03-01].

This page was created on Thu Feb 28 16:46:42 2008.