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DB00155 : l-citrulline

Approved nutraceutical l-citrulline ... 13 targets DB00155

Generic name: l-citrulline PDB Het Group: CIR
 
12 structures in PDB
Brand name(s): none.
Formula: C6H13N3O3
IUPAC Formula: (2s)-2-Amino-5-(Carbamoylamino)pentanoic acid
PDB name: Citrulline

13
There are 13 target proteins defined in DrugBank for this nutraceutical.
 6 
6 of these target proteins have one or more structures in the PDB.
 3 
There are 3 PDB structures of the nutraceutical molecule bound to its target protein.
 8 
There are 8 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: Q9ULC6 (PADI1_HUMAN)  -  Protein-arginine deiminase type-1
UniProt id: Q9ULC6    663 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: Q9ULW8 (PADI3_HUMAN)  -  Protein-arginine deiminase type-3
UniProt id: Q9ULW8    664 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 3:   UniProt id: Q9Y2J8 (PADI2_HUMAN)  -  Protein-arginine deiminase type-2
UniProt id: Q9Y2J8    665 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: Q9UM07 (PADI4_HUMAN)  -  Protein-arginine deiminase type-4
UniProt id: Q9UM07    662 a.a.  
1. 4dkt A     636 a.a. 634   X-ray 2.98 Å
  2. 2dew X     629 a.a. 626   X-ray 2.10 Å
  3. 3b1u A     628 a.a. 626   X-ray 2.10 Å
  4. 2dey X     628 a.a. 625   X-ray 2.25 Å
  5. 1wda A     628 a.a. 625   X-ray 2.30 Å
   more ...
There are no PDB entries containing l-citrulline bound to this target protein, although there are 12 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 5:   UniProt id: P00966 (ASSY_HUMAN)  -  Argininosuccinate synthase
UniProt id: P00966    411 a.a.  
2nz2 A   402 a.a. 402   X-ray 2.40 Å
The PDB contains 1 entry of l-citrulline bound to this target protein
DrugBank nutraceutical Target 6:   UniProt id: O95865 (DDAH2_HUMAN)  -  NG,NG-dimethylarginine dimethylaminohydrolase 2
UniProt id: O95865    285 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: Q5T6L4 (Q5T6L4_HUMAN)  -  Argininosuccinate synthase
UniProt id: Q5T6L4    412 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 8:   UniProt id: O94760 (DDAH1_HUMAN)  -  NG,NG-dimethylarginine dimethylaminohydrolase 1
UniProt id: O94760    284 a.a.  
2jai A   271 a.a. 271   X-ray 2.30 Å
The PDB contains 2 entries of l-citrulline bound to this target protein and 6 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 9:   UniProt id: P00480 (OTC_HUMAN)  -  Ornithine carbamoyltransferase, mitochondrial
UniProt id: P00480    353 a.a.  
1. 1oth A     321 a.a. 320   X-ray 1.85 Å
  2. 1c9y A     321 a.a. 320   X-ray 1.90 Å
  3. 1fvo A,B     321 a.a. 320   X-ray 2.60 Å
  4. 1ep9 A     320 a.a. 319   X-ray 2.40 Å
There are no PDB entries containing l-citrulline bound to this target protein, although there are 4 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 10:   UniProt id: P29475 (NOS1_HUMAN)  -  Nitric-oxide synthase, brain
UniProt id: P29475    1434 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 11:   UniProt id: P35228 (NOS2_HUMAN)  -  Nitric oxide synthase, inducible
UniProt id: P35228    1152 a.a.  
1. 3e7g A,B,C,D     421 a.a. 421   X-ray 2.20 Å
  2. 4nos A,B,C,D     421 a.a. 420   X-ray 2.25 Å
  3. 1nsi A,B,C,D     420 a.a. 420   X-ray 2.55 Å
  4. 2nsi A,B,C,D     420 a.a. 420   X-ray 3.00 Å
  5. 3ej8 A,B,C,D     421 a.a. 419   X-ray 2.55 Å
   more ...
There are no PDB entries containing l-citrulline bound to this target protein, although there are 8 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 12:   UniProt id: P29474 (NOS3_HUMAN)  -  Nitric-oxide synthase, endothelial
UniProt id: P29474    1202 a.a.  
1. 1m9m A,B     400 a.a. 400   X-ray 1.96 Å
  2. 1m9k A,B     400 a.a. 400   X-ray 2.01 Å
  3. 1m9q A,B     400 a.a. 400   X-ray 2.01 Å
  4. 3nos A,B     400 a.a. 400   X-ray 2.40 Å
  5. 1m9j A,B     400 a.a. 400   X-ray 2.43 Å
   more ...
There are no PDB entries containing l-citrulline bound to this target protein, although there are 10 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 13:   UniProt id: Q6TGC4 (PADI6_HUMAN)  -  Protein-arginine deiminase type-6
UniProt id: Q6TGC4    686 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  Secondary structure  Bound drug molecule

 

Other proteins with l-citrulline bound in the PDB

There are 7 "non-target" proteins in the PDB containing the l-citrulline molecule bound. That is, the UniProt code for the proteins is missing or does not match any of the nutraceutical targets listed above.

Protein 1:   UniProt id: P0A6E4 ()  -  Argininosuccinate synthase OS=Escherichia coli (strain K12) GN=argG PE=1 SV=2
UniProt id: P0A6E4    446 a.a.  
1kp3 A   439 a.a. 439   X-ray 2.00 Å
The PDB contains 1 entry of l-citrulline bound to this protein
Protein 2:   UniProt id: P23793 ()  -  Arginine deiminase OS=Mycoplasma arginini GN=arcA PE=1 SV=4
UniProt id: P23793    409 a.a.  
1lxy A,B   409 a.a. 409   X-ray 2.00 Å
The PDB contains 1 entry of l-citrulline bound to this protein
Protein 3:   UniProt id: P51541 ()  -  Arginine kinase OS=Limulus polyphemus PE=1 SV=1
UniProt id: P51541    356 a.a.  
4gvy A   356 a.a. 353   X-ray 2.09 Å
The PDB contains 1 entry of l-citrulline bound to this protein
Protein 4:   UniProt id: P56965 ()  -  N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 OS=Bos taurus GN=DDAH1 PE=1 SV=3
UniProt id: P56965    284 a.a.  
2c6z A   273 a.a. 273   X-ray 1.20 Å
The PDB contains 1 entry of l-citrulline bound to this protein
Protein 5:   UniProt id: P59846 ()  -  Argininosuccinate synthase OS=Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) GN=argG PE=1 SV=1
UniProt id: P59846    399 a.a.  
1. 1j1z A,B,C,D   386 a.a. 385   X-ray 2.10 Å
  2. 1j21 A,B,C,D   380 a.a. 379   X-ray 2.20 Å
The PDB contains 2 entries of l-citrulline bound to this protein
Protein 6:   UniProt id: Q8DCF5 ()  -  Ornithine carbamoyltransferase OS=Vibrio vulnificus (strain CMCP6) GN=argF PE=1 SV=1
UniProt id: Q8DCF5    334 a.a.  
4jqo A,B,C   338 a.a. 334   X-ray 2.08 Å
The PDB contains 1 entry of l-citrulline bound to this protein
Protein 7:   UniProt id: Q9I4E3 ()  -  N(G),N(G)-dimethylarginine dimethylaminohydrolase OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=PA1195 PE=1 SV=1
UniProt id: Q9I4E3    254 a.a.  
1h70 A   255 a.a. 253   X-ray 1.80 Å
The PDB contains 1 entry of l-citrulline 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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