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DB00122 : choline

Approved nutraceutical choline ... 7 targets DB00122

Generic name: choline PDB Het Group: CHT
 
28 structures in PDB
Brand name(s): none.
Formula: C5H14No
IUPAC Formula: (2-Hydroxyethyl)trimethylazanium
PDB name: Choline ion

7
There are 7 target proteins defined in DrugBank for this nutraceutical.
 2 
2 of these target proteins have one or more structures in the PDB.
 1 
There is 1 PDB structure of the nutraceutical molecule bound to its target protein.
 25 
There are 25 PDB structures containing the nutraceutical molecule bound to a protein that is not specified as a target.
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Target proteins

DrugBank nutraceutical Target 1:   UniProt id: Q9Y5K3 (PCY1B_HUMAN)  -  Choline-phosphate cytidylyltransferase B
UniProt id: Q9Y5K3    369 a.a.  
 
There are no structures of the target protein in the PDB (click icon on left for list of closest matches)
DrugBank nutraceutical Target 2:   UniProt id: P22303 (ACES_HUMAN)  -  Acetylcholinesterase
UniProt id: P22303    613 a.a.  
1. 4bdt A     563 a.a. 563   X-ray 3.10 Å
  2. 1clj       538 a.a. 538   Theor. model
  3. 1puv A     538 a.a. 538   Theor. model
  4. 1puw A     538 a.a. 538   Theor. model
  5. 2x8b A     536 a.a. 535   X-ray 2.95 Å
   more ...
There are no PDB entries containing choline bound to this target protein, although there are 16 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 3:   UniProt id: P49585 (PCY1A_HUMAN)  -  Choline-phosphate cytidylyltransferase A
UniProt id: P49585    367 a.a.  
 
There are no structures of the target protein in the PDB (click icon on left for list of closest matches)
DrugBank nutraceutical Target 4:   UniProt id: O14939 (PLD2_HUMAN)  -  Phospholipase D2
UniProt id: O14939    933 a.a.  
 
There are no structures of the target protein in the PDB (click icon on left for list of closest matches)
DrugBank nutraceutical Target 5:   UniProt id: P06276 (CHLE_HUMAN)  -  Cholinesterase
UniProt id: P06276    601 a.a.  
1p0m A   523 a.a. 520   X-ray 2.38 Å
The PDB contains 1 entry of choline bound to this target protein and 38 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 6:   UniProt id: Q13393 (PLD1_HUMAN)  -  Phospholipase D1
UniProt id: Q13393    1074 a.a.  
 
There are no structures of the target protein in the PDB (click icon on left for list of closest matches)
DrugBank nutraceutical Target 7:   UniProt id: Q8TCT1 (PHOP1_HUMAN)  -  Phosphoethanolamine/phosphocholine phosphatase
UniProt id: Q8TCT1    267 a.a.  
 
There are no structures of the target protein in the PDB (click icon on left for list of closest matches)

Key:    PfamA domain  PfamB domain  Secondary structure  Bound drug molecule

 

Other proteins with choline bound in the PDB

There are 16 "non-target" proteins in the PDB containing the choline molecule bound. That is, the UniProt code for the proteins is missing or does not match any of the nutraceutical targets listed above. Only 10 of the 16 proteins are listed below.

Protein 1:   UniProt id: C7MT25 ()  -  Transcriptional regulator OS=Saccharomonospora viridis (strain ATCC 15386 / DSM 43017 / JCM 3036 / NBRC 12207 / P101) GN=Svir_16270 PE=1 SV=1
UniProt id: C7MT25    286 a.a.  
4kwa A,B   193 a.a. 193   X-ray 1.80 Å
The PDB contains 1 entry of choline bound to this protein
Protein 2:   UniProt id: D0VWT1 ()  -  Choline kinase OS=Plasmodium knowlesi GN=PKH_134520 PE=1 SV=1
UniProt id: D0VWT1    368 a.a.  
3c5i A,B,C   343 a.a. 343   X-ray 2.20 Å
The PDB contains 1 entry of choline bound to this protein
Protein 3:   UniProt id: J1UPV3 ()  -  Lytic amidase OS=Streptococcus pneumoniae GA60080 GN=SPAR161_0006 PE=1 SV=1
  No Pfam domain assignments available for this protein.
4iwt A,B   146 a.a. 146   X-ray 2.60 Å
The PDB contains 1 entry of choline bound to this protein
Protein 4:   UniProt id: O32243 ()  -  Glycine betaine/carnitine/choline-binding protein OpuCC OS=Bacillus subtilis (strain 168) GN=opuCC PE=1 SV=1
UniProt id: O32243    302 a.a.  
3ppq A,B   271 a.a. 271   X-ray 1.91 Å
The PDB contains 1 entry of choline bound to this protein
Protein 5:   UniProt id: P00698 ()  -  Lysozyme C OS=Gallus gallus GN=LYZ PE=1 SV=1
UniProt id: P00698    146 a.a.  
4aga A   129 a.a. 129   X-ray 1.50 Å
The PDB contains 1 entry of choline bound to this protein
Protein 6:   UniProt id: P06653 ()  -  Autolysin OS=Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) GN=lytA PE=1 SV=2
UniProt id: P06653    317 a.a.  
1. 1hcx A,B   127 a.a. 126   X-ray 2.60 Å
  2. 1gvm A,B,C,D,E   127 a.a. 126   X-ray 2.80 Å
  3. 1h8g A,B   95 a.a. 94   X-ray 2.40 Å
The PDB contains 3 entries of choline bound to this protein
Protein 7:   UniProt id: P15057 ()  -  Lysozyme OS=Streptococcus phage Cp-1 GN=CPL1 PE=1 SV=2
UniProt id: P15057    338 a.a.  
1oba A   338 a.a. 337   X-ray 2.45 Å
The PDB contains 1 entry of choline bound to this protein
Protein 8:   UniProt id: P21836 ()  -  Acetylcholinesterase OS=Mus musculus GN=Ache PE=1 SV=1
UniProt id: P21836    613 a.a.  
2ha3 A,B   538 a.a. 538   X-ray 2.25 Å
The PDB contains 1 entry of choline bound to this protein
Protein 9:   UniProt id: P28329 ()  -  Choline O-acetyltransferase OS=Homo sapiens GN=CHAT PE=1 SV=4
UniProt id: P28329    747 a.a.  
2fy3 A   595 a.a. 580   X-ray 2.27 Å
The PDB contains 1 entry of choline bound to this protein
Protein 10:   UniProt id: P45723 ()  -  1-phosphatidylinositol phosphodiesterase OS=Staphylococcus aureus (strain Newman) GN=plc PE=1 SV=2
UniProt id: P45723    311 a.a.  
4i90 A   302 a.a. 299   X-ray 1.65 Å
The PDB contains 1 entry of choline bound to this protein

Key:    PfamA domain  Secondary structure  Bound drug molecule

The black crosses on the secondary structure diagrams indicate where the PDB and UniProt sequences differ.

Where there is more than one PDB model for a given UniProt sequence, the models are ordered by: 1. decreasing order of similarity to the UniProt sequence, 2. X-ray structures (in order of increasing resolution), NMR structures, and theoretical models. Clicking on any PDB code take you to the corresponding PDBsum page.

 

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