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DB00139 : succinic acid

Approved nutraceutical succinic acid ... 26 targets DB00139

Generic name: succinic acid PDB Het Group: SIN
 
118 structures in PDB
Brand name(s): katasuccin, kyselina jantarova.
Formula: C4H6O4
IUPAC Formula: Butanedioic acid
PDB name: Succinic acid

26
There are 26 target proteins defined in DrugBank for this nutraceutical.
 5 
5 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.
 94 
There are 94 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: Q13183 (S13A2_HUMAN)  -  Solute carrier family 13 member 2
UniProt id: Q13183    592 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: Q9BZW2 (S13A1_HUMAN)  -  Solute carrier family 13 member 1
UniProt id: Q9BZW2    595 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: Q96I99 (SUCB2_HUMAN)  -  Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial
UniProt id: Q96I99    432 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: O14521 (DHSD_HUMAN)  -  Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
UniProt id: O14521    159 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: O15460 (P4HA2_HUMAN)  -  Prolyl 4-hydroxylase subunit alpha-2
UniProt id: O15460    535 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: O60568 (PLOD3_HUMAN)  -  Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
UniProt id: O60568    738 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: O75936 (BODG_HUMAN)  -  Gamma-butyrobetaine dioxygenase
UniProt id: O75936    387 a.a.  
1. 3o2g A     386 a.a. 385   X-ray 1.78 Å
  2. 4bg1 A     385 a.a. 385   X-ray 1.89 Å
  3. 4bhi A     385 a.a. 385   X-ray 2.15 Å
  4. 4bgk A     385 a.a. 385   X-ray 2.18 Å
  5. 4c5w A     384 a.a. 384   X-ray 1.70 Å
   more ...
There are no PDB entries containing succinic acid bound to this target protein, although there are 11 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 8:   UniProt id: P13674 (P4HA1_HUMAN)  -  Prolyl 4-hydroxylase subunit alpha-1
UniProt id: P13674    533 a.a.  
1. 4bta A     237 a.a. 237   X-ray 2.95 Å
  2. 4bt9 A,B     236 a.a. 236   X-ray 1.90 Å
  3. 4btb A     231 a.a. 231   X-ray 1.90 Å
  4. 2yq8 A,B     225 a.a. 225   X-ray 2.99 Å
  5. 4bt8 A,B     222 a.a. 222   X-ray 2.20 Å
   more ...
There are no PDB entries containing succinic acid bound to this target protein, although there are 7 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 9:   UniProt id: P21912 (SDHB_HUMAN)  -  Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
  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 10:   UniProt id: P51649 (SSDH_HUMAN)  -  Succinate semialdehyde dehydrogenase, mitochondrial
UniProt id: P51649    534 a.a.  
2w8q A   485 a.a. 484   X-ray 2.40 Å
The PDB contains 1 entry of succinic acid bound to this target protein and 5 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 11:   UniProt id: Q99643 (C560_HUMAN)  -  Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
UniProt id: Q99643    169 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: P53597 (SUCA_HUMAN)  -  Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial
UniProt id: P53597    346 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: P55809 (SCOT1_HUMAN)  -  Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
UniProt id: P55809    519 a.a.  
3dlx A,B,C,D     470 a.a. 470   X-ray 2.20 Å
There are no PDB entries containing succinic acid bound to this target protein, although there is 1 entry of the target protein in the PDB (see above).
DrugBank nutraceutical Target 14:   UniProt id: Q02809 (PLOD1_HUMAN)  -  Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
UniProt id: Q02809    727 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: Q12797 (ASPH_HUMAN)  -  Aspartyl/asparaginyl beta-hydroxylase
UniProt id: Q12797    757 a.a.  
3rcq A     197 a.a. 197   X-ray 2.05 Å
There are no PDB entries containing succinic acid bound to this target protein, although there is 1 entry of the target protein in the PDB (see above).
DrugBank nutraceutical Target 16:   UniProt id: Q32P28 (P3H1_HUMAN)  -  Prolyl 3-hydroxylase 1
UniProt id: Q32P28    736 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: Q8IVL5 (P3H2_HUMAN)  -  Prolyl 3-hydroxylase 2
UniProt id: Q8IVL5    708 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: Q8IVL6 (P3H3_HUMAN)  -  Prolyl 3-hydroxylase 3
UniProt id: Q8IVL6    736 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 19:   UniProt id: Q9BXA5 (SUCR1_HUMAN)  -  Succinate receptor 1
UniProt id: Q9BXA5    334 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 20:   UniProt id: Q9BYC2 (SCOT2_HUMAN)  -  Succinyl-CoA:3-ketoacid-coenzyme A transferase 2, mitochondrial
UniProt id: Q9BYC2    517 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: Q9NVH6 (TMLH_HUMAN)  -  Trimethyllysine dioxygenase, mitochondrial
UniProt id: Q9NVH6    421 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 22:   UniProt id: Q9P2R7 (SUCB1_HUMAN)  -  Succinyl-CoA ligase [ADP-forming] beta-chain, mitochondrial
UniProt id: Q9P2R7    463 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: Q9UBX3 (DIC_HUMAN)  -  Mitochondrial dicarboxylate carrier
UniProt id: Q9UBX3    287 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: P31040 (SDHA_HUMAN)  -  Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
  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 25:   UniProt id: O14756 (H17B6_HUMAN)  -  Oxidoreductase
UniProt id: O14756    317 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 26:   UniProt id: Q8WWT9 (S13A3_HUMAN)  -  Solute carrier family 13 member 3
UniProt id: Q8WWT9    602 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 succinic acid bound in the PDB

There are 72 "non-target" proteins in the PDB containing the succinic acid 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 72 proteins are listed below.

Protein 1:   UniProt id: A3QCW5 ()  -  TRAP dicarboxylate transporter, DctP subunit OS=Shewanella loihica (strain ATCC BAA-1088 / PV-4) GN=Shew_1446 PE=1 SV=1
UniProt id: A3QCW5    335 a.a.  
4oa4 A,B,C,D   304 a.a. 304   X-ray 1.60 Å
The PDB contains 1 entry of succinic acid bound to this protein
Protein 2:   UniProt id: A6P7M9 ()  -  Sphingomyelinase C OS=Streptomyces griseocarneus GN=smc PE=4 SV=1
UniProt id: A6P7M9    338 a.a.  
3wcx A   291 a.a. 291   X-ray 2.00 Å
The PDB contains 1 entry of succinic acid bound to this protein
Protein 3:   UniProt id: B1UL22 ()  -  Phenazine biosynthesis protein, PhzF family OS=Bacillus anthracis str. A0174 GN=BAO_3465 PE=1 SV=1
UniProt id: B1UL22    298 a.a.  
3edn A,B   299 a.a. 298   X-ray 1.50 Å
The PDB contains 1 entry of succinic acid bound to this protein
Protein 4:   UniProt id: C0QQ26 ()  -  Metal dependent phosphohydrolase OS=Persephonella marina (strain DSM 14350 / EX-H1) GN=PERMA_0986 PE=1 SV=1
UniProt id: C0QQ26    363 a.a.  
1. 4mcw A,B   361 a.a. 357   X-ray 2.03 Å
  2. 4me4 A,B   361 a.a. 357   X-ray 2.55 Å
  3. 4mdz A,B   361 a.a. 357   X-ray 2.68 Å
The PDB contains 3 entries of succinic acid bound to this protein
Protein 5:   UniProt id: C7C419 ()  -  Serpin peptidase inhibitor, clade H (Heat shock protein 47), member 1, (Collagen binding protein 1) OS=Canis familiaris GN=SERPINH1 PE=1 SV=1
UniProt id: C7C419    417 a.a.  
4awr A,B,C,D,...   375 a.a. 374   X-ray 2.70 Å
The PDB contains 1 entry of succinic acid bound to this protein
Protein 6:   UniProt id: D0ZHW1 ()  -  Conjugative transfer: regulation OS=Salmonella typhimurium (strain 14028s / SGSC 2262) GN=traJ PE=1 SV=1
UniProt id: D0ZHW1    227 a.a.  
4ew7 A   113 a.a. 113   X-ray 1.67 Å
The PDB contains 1 entry of succinic acid bound to this protein
Protein 7:   UniProt id: D1AZL7 ()  -  TRAP dicarboxylate transporter, DctP subunit OS=Sulfurospirillum deleyianum (strain ATCC 51133 / DSM 6946 / 5175) GN=Sdel_0447 PE=1 SV=1
UniProt id: D1AZL7    328 a.a.  
4ovs A,B   310 a.a. 309   X-ray 1.80 Å
The PDB contains 1 entry of succinic acid bound to this protein
Protein 8:   UniProt id: D9PZ08 ()  -  Beta-galactosidase OS=Acidilobus saccharovorans (strain DSM 16705 / VKM B-2471 / 345-15) GN=ASAC_1390 PE=1 SV=1
UniProt id: D9PZ08    489 a.a.  
4ha4 A   489 a.a. 489   X-ray 1.37 Å
The PDB contains 1 entry of succinic acid bound to this protein
Protein 9:   UniProt id: E2RHY7 ()  -  Uncharacterized protein OS=Canis familiaris GN=SERPINH1 PE=1 SV=1
UniProt id: E2RHY7    417 a.a.  
3zha A,B,C,D,...   380 a.a. 377   X-ray 2.55 Å
The PDB contains 1 entry of succinic acid bound to this protein
Protein 10:   UniProt id: F6XHE4 ()  -  Uncharacterized protein OS=Ciona intestinalis GN=vsp PE=1 SV=1
UniProt id: F6XHE4    569 a.a.  
4g7v S   136 a.a. 135   X-ray 2.50 Å
The PDB contains 1 entry of succinic acid 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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