spacer
spacer

Search 

DB00145 : glycine

Approved nutraceutical glycine ... 34 targets DB00145

Generic name: glycine PDB Het Group: GLY
 
107 structures in PDB
Brand name(s): aciport, glicoamin, glycocoll, glycolixir, glycosthene, gyn-hydralin, padil.
Formula: C2H5No2
IUPAC Formula: 2-Aminoacetic acid
PDB name: Glycine

34
There are 34 target proteins defined in DrugBank for this nutraceutical.
 8 
8 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.
 77 
There are 77 PDB structures containing the nutraceutical molecule bound to a protein that is not specified as a target.
Links  
DrugBank
ChEBI
KEGG drug
PubChem
MSDChem
Ligand Expo
HIC-Up
Information  
Pharmacology
Indication
Action

 

Target proteins

DrugBank nutraceutical Target 1:   UniProt id: Q14957 (NMDE3_HUMAN)  -  Glutamate [NMDA] receptor subunit epsilon-3
UniProt id: Q14957    1233 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: Q53ET4 (Q53ET4_HUMAN)  -  Serine hydroxymethyltransferase 2
UniProt id: Q53ET4    504 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: Q5BJF5 (Q5BJF5_HUMAN)  -  SHMT2 protein
UniProt id: Q5BJF5    480 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: Q5HYG8 (Q5HYG8_HUMAN)  -  Hypothetical protein DKFZp686P09201
UniProt id: Q5HYG8    483 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: Q6IB77 (GLYAT_HUMAN)  -  Glycine N-acyltransferase
UniProt id: Q6IB77    296 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 6:   UniProt id: Q7Z2H8 (S36A1_HUMAN)  -  Proton-coupled amino acid transporter 1
UniProt id: Q7Z2H8    476 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: Q8N1A5 (GLYM_HUMAN)  -  SHMT2 protein
  No Pfam domain assignments available for this protein.
 
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: Q8WU03 (GLYL2_HUMAN)  -  Glycine N-acyltransferase-like protein 2
UniProt id: Q8WU03    294 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 9:   UniProt id: Q969I3 (GLYL1_HUMAN)  -  Glycine N-acyltransferase-like protein 1
UniProt id: Q969I3    302 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 10:   UniProt id: Q9BYV1 (AGT2_HUMAN)  -  Alanine--glyoxylate aminotransferase 2, mitochondrial
UniProt id: Q9BYV1    514 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: O75600 (KBL_HUMAN)  -  2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial
UniProt id: O75600    419 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 12:   UniProt id: Q9H598 (VIAAT_HUMAN)  -  Vesicular inhibitory amino acid transporter
UniProt id: Q9H598    525 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 13:   UniProt id: Q9P0Z9 (SOX_HUMAN)  -  Peroxisomal sarcosine oxidase
UniProt id: Q9P0Z9    390 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 14:   UniProt id: Q9Y345 (SC6A5_HUMAN)  -  Sodium- and chloride-dependent glycine transporter 2
UniProt id: Q9Y345    797 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 15:   UniProt id: O60391 (NMD3B_HUMAN)  -  Glutamate [NMDA] receptor subunit 3B
UniProt id: O60391    1043 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 16:   UniProt id: P23378 (GCSP_HUMAN)  -  Glycine dehydrogenase [decarboxylating], mitochondrial
UniProt id: P23378    1020 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 17:   UniProt id: P48067 (SC6A9_HUMAN)  -  Sodium- and chloride-dependent glycine transporter 1
UniProt id: P48067    706 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 18:   UniProt id: P23415 (GLRA1_HUMAN)  -  Glycine receptor subunit alpha-1
UniProt id: P23415    456 a.a.  
1. 2m6b A     150 a.a. 129   NMR  
  2. 2m6i A,B,C,D,E     150 a.a. 129   NMR  
  3. 1vry A     61 a.a. 58   NMR  
  4. 1zhd A     61 a.a. 58   NMR  
  5. 1mot A     28 a.a. 28   NMR  
There are no PDB entries containing glycine bound to this target protein, although there are 5 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 19:   UniProt id: P21549 (SPYA_HUMAN)  -  Serine--pyruvate aminotransferase
UniProt id: P21549    391 a.a.  
1. 3imz A,C     387 a.a. 387   X-ray 2.35 Å
  2. 1h0c A     386 a.a. 386   X-ray 2.50 Å
  3. 3r9a A,C     386 a.a. 385   X-ray 2.35 Å
  4. 1j04 A     386 a.a. 384   X-ray 2.60 Å
  5. 4i8a A,B,C,D     386 a.a. 384   X-ray 2.90 Å
   more ...
There are no PDB entries containing glycine 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 20:   UniProt id: P48167 (GLRB_HUMAN)  -  Glycine receptor subunit beta
UniProt id: P48167    497 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 21:   UniProt id: P34896 (GLYC_HUMAN)  -  Serine hydroxymethyltransferase, cytosolic
UniProt id: P34896    482 a.a.  
1bj4 A     470 a.a. 467   X-ray 2.65 Å
There are no PDB entries containing glycine bound to this target protein, although there is 1 entry of the target protein in the PDB (see above).
DrugBank nutraceutical Target 22:   UniProt id: P13196 (HEM1_HUMAN)  -  5-aminolevulinate synthase, nonspecific, mitochondrial
UniProt id: P13196    640 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 23:   UniProt id: O75311 (GLRA3_HUMAN)  -  Glycine receptor subunit alpha-3
UniProt id: O75311    464 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 24:   UniProt id: P23416 (GLRA2_HUMAN)  -  Glycine receptor subunit alpha-2
UniProt id: P23416    452 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 25:   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 glycine 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 26:   UniProt id: P34897 (GLYM_HUMAN)  -  Serine hydroxymethyltransferase, mitochondrial
UniProt id: P34897    503 a.a.  
1. 3ou5 A     422 a.a. 422   X-ray 2.04 Å
  2. 2a7v A     420 a.a. 420   X-ray 2.04 Å
There are no PDB entries containing glycine 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 27:   UniProt id: P50440 (GATM_HUMAN)  -  Glycine amidinotransferase, mitochondrial
UniProt id: P50440    422 a.a.  
5jdw A   360 a.a. 360   X-ray 2.60 Å
The PDB contains 1 entry of glycine bound to this target protein and 11 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 28:   UniProt id: P22557 (HEM0_HUMAN)  -  5-aminolevulinate synthase, erythroid-specific, mitochondrial
UniProt id: P22557    587 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 29:   UniProt id: P23434 (GCSH_HUMAN)  -  Glycine cleavage system H protein, mitochondrial
UniProt id: P23434    173 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 30:   UniProt id: P41250 (SYG_HUMAN)  -  Glycyl-tRNA synthetase
UniProt id: P41250    738 a.a.  
1. 2zt7 A   530 a.a. 530   X-ray 2.70 Å
  2. 4kr3 A   466 a.a. 465   X-ray 3.23 Å
The PDB contains 2 entries of glycine bound to this target protein and 12 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 31:   UniProt id: Q12879 (NMDE1_HUMAN)  -  Glutamate [NMDA] receptor subunit epsilon-1
UniProt id: Q12879    1464 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 32:   UniProt id: Q14032 (BAAT_HUMAN)  -  Bile acid CoA:amino acid N-acyltransferase
UniProt id: Q14032    418 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 33:   UniProt id: Q14330 (GPR18_HUMAN)  -  N-arachidonyl glycine receptor
UniProt id: Q14330    331 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 34:   UniProt id: P48637 (GSHB_HUMAN)  -  Glutathione synthetase
UniProt id: P48637    473 a.a.  
2hgs A     472 a.a. 472   X-ray 2.10 Å
There are no PDB entries containing glycine bound to this target protein, although there is 1 entry of the target protein in the PDB (see above).

Key:    PfamA domain  PfamB domain  Secondary structure  Bound drug molecule

 

Other proteins with glycine bound in the PDB

There are 52 "non-target" proteins in the PDB containing the glycine 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 52 proteins are listed below.

Protein 1:   UniProt id: B1VBB0 ()  -  Chitinase 60 OS=Vibrio marinus GN=chi60 PE=1 SV=1
UniProt id: B1VBB0    549 a.a.  
1. 4mb4 A   528 a.a. 525   X-ray 1.48 Å
  2. 4mb3 A   528 a.a. 525   X-ray 1.55 Å
  3. 4mb5 A   528 a.a. 525   X-ray 1.64 Å
The PDB contains 3 entries of glycine bound to this protein
Protein 2:   UniProt id: O15305 ()  -  Phosphomannomutase 2 OS=Homo sapiens GN=PMM2 PE=1 SV=1
UniProt id: O15305    245 a.a.  
1. 2amy A   240 a.a. 240   X-ray 2.09 Å
  2. 2q4r A   240 a.a. 240   X-ray 2.09 Å
The PDB contains 2 entries of glycine bound to this protein
Protein 3:   UniProt id: O67323 ()  -  Alanine--tRNA ligase OS=Aquifex aeolicus (strain VF5) GN=alaS PE=1 SV=1
UniProt id: O67323    866 a.a.  
1yft A   448 a.a. 444   X-ray 2.23 Å
The PDB contains 1 entry of glycine bound to this protein
Protein 4:   UniProt id: P00730 ()  -  Carboxypeptidase A1 OS=Bos taurus GN=CPA1 PE=1 SV=3
UniProt id: P00730    418 a.a.  
4cpa A,B   307 a.a. 298   X-ray 2.50 Å
The PDB contains 1 entry of glycine bound to this protein
Protein 5:   UniProt id: P01391 ()  -  Alpha-elapitoxin-Nk2a OS=Naja kaouthia PE=1 SV=1
UniProt id: P01391    70 a.a.  
4aea A,B   67 a.a. 66   X-ray 1.94 Å
The PDB contains 1 entry of glycine bound to this protein
Protein 6:   UniProt id: P01909 ()  -  HLA class II histocompatibility antigen, DQ alpha 1 chain OS=Homo sapiens GN=HLA-DQA1 PE=1 SV=1
UniProt id: P01909    253 a.a.  
1uvq A   182 a.a. 157   X-ray 1.80 Å
The PDB contains 1 entry of glycine bound to this protein
Protein 7:   UniProt id: P03369 ()  -  Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2) GN=gag-pol PE=1 SV=3
UniProt id: P03369    1436 a.a.  
2fnt A,B   99 a.a. 96   X-ray 1.44 Å
The PDB contains 1 entry of glycine bound to this protein
Protein 8:   UniProt id: P07511 ()  -  Serine hydroxymethyltransferase, cytosolic OS=Oryctolagus cuniculus GN=SHMT1 PE=1 SV=2
UniProt id: P07511    483 a.a.  
1ls3 A,B,C,D   465 a.a. 465   X-ray 2.70 Å
The PDB contains 1 entry of glycine bound to this protein
Protein 9:   UniProt id: P09331 ()  -  Exfoliative toxin A OS=Staphylococcus aureus GN=eta PE=1 SV=1
UniProt id: P09331    279 a.a.  
1exf A   241 a.a. 241   X-ray 2.10 Å
The PDB contains 1 entry of glycine bound to this protein
Protein 10:   UniProt id: P15309 ()  -  Prostatic acid phosphatase OS=Homo sapiens GN=ACPP PE=1 SV=3
UniProt id: P15309    385 a.a.  
1cvi A,B,C,D   342 a.a. 342   X-ray 3.20 Å
The PDB contains 1 entry of glycine 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.

 

Structure selection

Use the checkboxes above to select the structure(s) of interest, and then press the required button below to view:
View 3D structure
Select preferred viewer and click on 3D struct button
AstexViewer™@MSD-EBI
RasMol
STRAP multiple alignment viewer
LIGPLOT diagrams
Press button below for LIGPLOT diagrams of nutraceutical-protein interactions in all selected structures above.

  spacer

spacer