Rasmol image by Barani
HIC-Up
Diagram from MSDchem

| Coordinates | Visualisation | Dictionaries | Miscellaneous | Off-site | Rest |

Compound: ACA
Formula: C6 H13 N O2
Name(s):
  • 6-aminohexanoic acid
  • aminocaproic acid
Experimental: PDB entry 2dcf | Residue 501 | Resolution 1.40 Å | MSD | RCSB | EDS | PDBsum | PDBREPORT | OCA | JenaLib | MMDB
Also in: 14 other PDB entries, namely 3KIV | 1CEA | 1VQ8 | 2PK4 | 1VQK | 1VQ9 | 1VQN | 1VQ6 | 1M90 | 1KQS | 1HPK | 1ILP | 1ILQ | 1PK2 |

Coordinates
PDB file (".pdb"; ideal coordinates for 9 atoms from MSDchem)
PDB file (".pdb"; experimental coordinates for 4 atoms from PDB entry 2dcf)
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, 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 could not be generated
TNT dictionary file

Miscellaneous
Disclaimer
EDS statistics
HETZE log file (rudimentary quality assessment)
Connection table file
List of 2 superstructures

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 "ACA" in the PDB to the ideal structure ValLigURL (Uppsala University)
Go! View model and electron density for "ACA 501" in PDB entry 2dcf (opens Java viewer) EDS (Uppsala University)
Go! Main EDS page for parent PDB entry 2dcf EDS (Uppsala University)
Description
Generate hydrogens and dictionaries (MDL, GROMOS87, GROMACS, REFMAC5, SYBYL2, AUTODOCK, WHAT IF, HEX, CNS, O, and SHELX) for "ACA" using the clean PDB file as input PRODRG2 server (University of Dundee)
Go! Ligand chemistry for "ACA" in MSDchem MSD (EBI)
Go! Ligand chemistry for "ACA" from MSDchem in XML format MSD (EBI)
Go! Information about "ACA" in ChEBI ChEBI (EBI)
Run Babel to convert the clean PDB file of "ACA" to canonical SMILES and other formats ChemDB (UC Irvine)
Go! Ligand chemistry for ACA in MSDchem@RCSB MSDchem@RCSB (Rutgers)
Go! CIF dictionary for "ACA" Ligand Depot (Rutgers)
PDB entries
Go! List of all PDB entries containing "ACA" from MSDmotif MSD (EBI)
Go! List of unique PDB entries containing "ACA" from MSDmotif MSD (EBI)
Go! Download all instances of "ACA" in the PDB including their environment (tar-file) MSD (EBI)
Go! List of PDB entries containing "ACA" PDBsum (EBI)
Go! List of PDB entries containing "ACA" RCSB
Go! List of PDB entries containing "ACA" Ligand Depot (Rutgers)
Go! List of PDB entries containing "ACA" DHC JenaLib (Fritz Lipmann Institute)
Go! List of PDB entries containing "ACA" OCA (Weizmann Institute)
Structural biology
Go! List PDB entries for which "ACA" is a cognate ligand PROCOGNATE (EBI)
Go! Statistics about protein residues that interact with "ACA" from MSDmotif MSD (EBI)
Go! Statistics about nucleic acid residues that interact with "ACA" from MSDmotif MSD (EBI)
Go! Statistics about other ligands that interact with "ACA" from MSDmotif MSD (EBI)
Go! Statistics about PROSITE motifs that interact with "ACA" from MSDmotif MSD (EBI)
Go! Statistics about small 3D motifs that interact with "ACA" from MSDmotif MSD (EBI)
Go! Statistics about secondary structure elements that interact with "ACA" from MSDmotif MSD (EBI)
Search for "ACA" in ReliBase ReliBase (CCDC)
Go! List of PDB entries containing "ACA" and interacting residues FireDB (Spain)
Go! Search for "ACA" in the PDB-Ligand database PDB-Ligand (Korea)
Miscellaneous
Go! Search for "ACA" in the PubChem compound database PubChem (NCBI)
Go! Search for "C6 H13 N O2" in the Chemistry Webbook Chemistry Webbook (NIST)
Search for "6-aminohexanoic acid" in the ChemDB compound database ChemDB (UC Irvine)
Go! Search for "6-aminohexanoic acid" in the KEGG-Ligand database KEGG-Ligand (Kyoto University)
Go! Search for "6-aminohexanoic acid" with Google Google

Summary of HETZE report :

 Residue type                   : (ACA) 
 Identifier                     : ( 1409) 
 Segment ID                     : ( ) 

 Nr of atoms                    : (       9) 
 List of elements (from file)   : ( C6 H13 N O2) 
 Deduced formula                : (C6 N1 O2) 
 Guestimated total nr of Hs     : (      12) 
 Nr of extra examples           : (       0) 

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

 Nr of bonds found              : (       8) 
 ... bonds without ideal value  : (       0) 
 ... bonds near ideal value     : (       8) 
 ... bonds far from ideal value : (       0) 
          -"-                 % : (   0.000) 

 Nr of angles found             : (       8) 

 Nr of dihedrals found          : (       6) 

 Nr of atoms with impropers     : (       1) 
 ... imprs far from ideal value : (       0) 
          -"-                 % : (   0.000) 

 Nr of flat planes              : (       1) 


2D structure diagram from MSDchem

2D structure diagram from MSDchem@RCSB

3D Image generated with LIGPLOT

RASMOL image provided by Barani


  • This page is part of the HIC-Up site (Hetero-compound Information Centre - Uppsala).
  • © 1997 - 2008, Gerard Kleywegt, Uppsala, Sweden. All rights reserved.
  • Please read this before contacting Gerard.
  • Sign or view the HIC-Up guestbook - thanks !
  • HIC-Up release 12.1 [2008-03-01].

This page was created on Thu Feb 28 16:07:06 2008.