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DB00118 : s-adenosylmethionine

Approved nutraceutical s-adenosylmethionine ... 6 targets DB00118

Generic name: s-adenosylmethionine PDB Het Group: SAM
 
268 structures in PDB
Brand name(s): same rx-mood, sam-sulfate.
Formula: C15H23N6O5S
IUPAC Formula: [(3s)-3-Amino-3-Carboxypropyl]({[(2s,3s,4r,5r)-5-(6-Amino-9h-Purin-9-Yl)-3,4-Dihydroxyoxolan-2-
Yl]methyl})methylsulfanium
PDB name: S-Adenosylmethionine

6
There are 6 target proteins defined in DrugBank for this nutraceutical.
 6 
6 of these target proteins have one or more structures in the PDB.
 12 
There are 12 PDB structures of the nutraceutical molecule bound to its target protein.
 234 
There are 234 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: Q14749 (GNMT_HUMAN)  -  Glycine N-methyltransferase
UniProt id: Q14749    294 a.a.  
1. 1r74 A,B     275 a.a. 275   X-ray 2.55 Å
  2. 2azt A,B     276 a.a. 275   X-ray 2.70 Å
There are no PDB entries containing s-adenosylmethionine bound to this target protein, although there are 2 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 2:   UniProt id: P17707 (DCAM_HUMAN)  -  S-adenosylmethionine decarboxylase proenzyme
UniProt id: P17707    333 a.a.  
1. 1msv A,B     319 a.a. 318   X-ray 1.75 Å
  2. 1jl0 A,B     310 a.a. 308   X-ray 1.50 Å
  3. 3h0w B     61 a.a. 61   X-ray 1.81 Å
  4. 3dz4 B     61 a.a. 61   X-ray 1.84 Å
  5. 1i7b B     61 a.a. 61   X-ray 1.90 Å
   more ...
There are no PDB entries containing s-adenosylmethionine bound to this target protein, although there are 25 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 3:   UniProt id: P31153 (METK2_HUMAN)  -  S-adenosylmethionine synthetase isoform type-2
UniProt id: P31153    394 a.a.  
1. 2hj2 A,B   380 a.a. 380   X-ray 1.03 Å
  2. 2p02 A   380 a.a. 380   X-ray 1.21 Å
  3. 4ndn A,C   362 a.a. 362   X-ray 2.34 Å
  4. 4ktt A,C   360 a.a. 360   X-ray 2.59 Å
The PDB contains 6 entries of s-adenosylmethionine bound to this target protein
DrugBank nutraceutical Target 4:   UniProt id: P35520 (CBS_HUMAN)  -  Cystathionine beta-synthase
UniProt id: P35520    550 a.a.  
4uuu A   137 a.a. 130   X-ray 1.71 Å
The PDB contains 2 entries of s-adenosylmethionine bound to this target protein and 8 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 5:   UniProt id: Q00266 (METK1_HUMAN)  -  S-adenosylmethionine synthetase isoform type-1
UniProt id: Q00266    394 a.a.  
2obv A   384 a.a. 381   X-ray 2.05 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this target protein
DrugBank nutraceutical Target 6:   UniProt id: P21964 (COMT_HUMAN)  -  Catechol O-methyltransferase
UniProt id: P21964    270 a.a.  
1. 3bwm A   214 a.a. 214   X-ray 1.98 Å
  2. 3bwy A   214 a.a. 213   X-ray 1.30 Å
  3. 3a7e A   212 a.a. 212   X-ray 2.80 Å
The PDB contains 3 entries of s-adenosylmethionine bound to this target protein and 6 entries of this target protein in all (click on orange, plus icon for list).

Key:    PfamA domain  Secondary structure  Bound drug molecule

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

 

Other proteins with s-adenosylmethionine bound in the PDB

There are 173 "non-target" proteins in the PDB containing the s-adenosylmethionine 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 173 proteins are listed below.

Protein 1:   UniProt id: A0EKU1 ()  -  Polyprotein OS=Meaban virus PE=1 SV=1
UniProt id: A0EKU1    3420 a.a.  
2oxt A,B,C,D   265 a.a. 265   X-ray 2.90 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this protein
Protein 2:   UniProt id: A3DDA2 ()  -  rRNA methylase OS=Clostridium thermocellum (strain ATCC 27405 / DSM 1237) GN=Cthe_0696 PE=1 SV=1
UniProt id: A3DDA2    187 a.a.  
3eey A,B,C,D,...   195 a.a. 186   X-ray 2.20 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this protein
Protein 3:   UniProt id: A4X3Q0 ()  -  Adenosyl-chloride synthase OS=Salinispora tropica (strain ATCC BAA-916 / DSM 44818 / CNB-440) GN=salL PE=1 SV=1
UniProt id: A4X3Q0    282 a.a.  
2q6o A,B   269 a.a. 268   X-ray 2.00 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this protein
Protein 4:   UniProt id: A5K867 ()  -  Phosphoethanolamine N-methyltransferase, putative OS=Plasmodium vivax (strain Salvador I) GN=PVX_083045 PE=1 SV=1
UniProt id: A5K867    263 a.a.  
4iv0 A,B   263 a.a. 263   X-ray 1.40 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this protein
Protein 5:   UniProt id: A6L5C0 ()  -  Uncharacterized protein OS=Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / NCTC 11154) GN=BVU_3255 PE=1 SV=1
UniProt id: A6L5C0    261 a.a.  
3t7s A,B,C,D   246 a.a. 246   X-ray 2.20 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this protein
Protein 6:   UniProt id: A8C927 ()  -  16S rRNA (adenine(1408)-N(1))-methyltransferase OS=Escherichia coli GN=npmA PE=1 SV=1
UniProt id: A8C927    218 a.a.  
1. 3mte A,B   219 a.a. 218   X-ray 1.80 Å
  2. 3p2k A,B,C,D   197 a.a. 197   X-ray 2.70 Å
The PDB contains 2 entries of s-adenosylmethionine bound to this protein
Protein 7:   UniProt id: A9CKD6 ()  -  SAM dependent methyltransferase OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=Atu0340 PE=1 SV=1
UniProt id: A9CKD6    309 a.a.  
2igt A,B,C   313 a.a. 306   X-ray 1.89 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this protein
Protein 8:   UniProt id: A9LIE0 ()  -  Polyprotein OS=Dengue virus 3 PE=4 SV=1
UniProt id: A9LIE0    3389 a.a.  
1. 4ctj A,C   257 a.a. 257   X-ray 1.47 Å
  2. 4ctk A,C   257 a.a. 257   X-ray 1.53 Å
The PDB contains 2 entries of s-adenosylmethionine bound to this protein
Protein 9:   UniProt id: B3L8G9 ()  -  Phosphoethanolamine N-methyltransferase,putative OS=Plasmodium knowlesi (strain H) GN=PKH_121150 PE=1 SV=1
UniProt id: B3L8G9    263 a.a.  
4iv8 A,B   245 a.a. 245   X-ray 1.90 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this protein
Protein 10:   UniProt id: B5L6K6 ()  -  Methyltransferase OS=Micromonospora chalcea PE=1 SV=1
UniProt id: B5L6K6    413 a.a.  
3ndi A   405 a.a. 405   X-ray 1.50 Å
The PDB contains 1 entry of s-adenosylmethionine bound to this protein

Key:    PfamA domain  PfamB 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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