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DB00126 : vitamin c

Approved nutraceutical vitamin c ... 26 targets DB00126

Generic name: vitamin c PDB Het Group: ASC
 
23 structures in PDB
Brand name(s): adenex, allercorb, antiscorbic vitamin, antiscorbutic vitamin, arco-cee, ascoltin, ascor-b.i.d., ascorb, ascorbajen, ascorbicab, ascorbicap, ascorbicin, ascorbin, ascorbutina, ascorin, ascorteal, ascorvit, c-level, c-long, c-quin, c-span, c-vimin, cantan, cantaxin, catavin c, ce lent, cebicure, cebid, cebion, cebione, cecon, cee-caps td, cee-vite, cegiolan, ceglion, celaskon, celin, cemagyl, cemill, cenetone, cenolate, cereon, cergona, cescorbat, cetamid, cetane, cetane-caps tc, cetane-caps td, cetebe, cetemican, cevalin, cevatine, cevex, cevi-bid, cevimin, cevital, cevitamic acid, cevitamin, cevitan, cevitex, cewin, ciamin, cipca, citriscorb, colascor, concemin, davitamon c, duoscorb, hicee, hybrin, ido-c, kyselina askorbova, laroscorbine, lemascorb, liqui-cee, meri-c, natrascorb, planavit c, proscorbin, redoxon, ribena, roscorbic, scorbacid, scorbu-c, secorbate, sodascorbate, testascorbic, vicelat, vicin, vicomin c, viforcit, viscorin, vitace, vitacee, vitacimin, vitacin, vitamisin, vitascorbol, xitix.
Formula: C6H8O6
IUPAC Formula: (5r)-5-[(1s)-1,2-Dihydroxyethyl]-3,4-Dihydroxy-2,5-Dihydrofuran-2-One
PDB name: Ascorbic acid

26
There are 26 target proteins defined in DrugBank for this nutraceutical.
 10 
10 of these target proteins have one or more structures in the PDB.
 2 
There are 2 PDB structures of the nutraceutical molecule bound to its target protein.
 17 
There are 17 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: P19021 (AMD_HUMAN)  -  Peptidyl-glycine alpha-amidating monooxygenase
UniProt id: P19021    973 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: 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 vitamin c 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 3:   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 4:   UniProt id: Q6N063 (OGFD2_HUMAN)  -  Hypothetical protein DKFZp686H15154
UniProt id: Q6N063    350 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: Q6NS38 (ALKB2_HUMAN)  -  Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
UniProt id: Q6NS38    260 a.a.  
1. 3s57 A     204 a.a. 199   X-ray 1.60 Å
  2. 3s5a A     204 a.a. 199   X-ray 1.70 Å
  3. 3h8r A     204 a.a. 199   X-ray 1.77 Å
  4. 3h8x A     204 a.a. 199   X-ray 1.95 Å
  5. 3btx A     204 a.a. 199   X-ray 2.00 Å
   more ...
There are no PDB entries containing vitamin c bound to this target protein, although there are 18 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 6:   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 7:   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 8:   UniProt id: Q8N543 (OGFD1_HUMAN)  -  2-oxoglutarate and iron-dependent oxygenase domain containing 1
UniProt id: Q8N543    541 a.a.  
1. 4nhy A,B,C,D     461 a.a. 461   X-ray 2.60 Å
  2. 4nhx A     457 a.a. 457   X-ray 2.10 Å
There are no PDB entries containing vitamin c 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 9:   UniProt id: Q96KS0 (EGLN2_HUMAN)  -  Egl nine homolog 2
UniProt id: Q96KS0    407 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: Q96Q83 (ALKB3_HUMAN)  -  Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
UniProt id: Q96Q83    285 a.a.  
2iuw A     204 a.a. 200   X-ray 1.50 Å
There are no PDB entries containing vitamin c bound to this target protein, although there is 1 entry of the target protein in the PDB (see above).
DrugBank nutraceutical Target 11:   UniProt id: P09848 (LPH_HUMAN)  -  Lactase-phlorizin hydrolase
UniProt id: P09848    1927 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: Q9BY66 (KDM5D_HUMAN)  -  Jumonji/ARID domain-containing protein 1D
UniProt id: Q9BY66    1538 a.a.  
1. 2yqe A     100 a.a. 93   NMR  
  2. 2e6r A     92 a.a. 79   NMR  
There are no PDB entries containing vitamin c 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 13:   UniProt id: Q9GZT9 (EGLN1_HUMAN)  -  Egl nine homolog 1
UniProt id: Q9GZT9    425 a.a.  
1. 4kbz A     231 a.a. 230   X-ray 2.15 Å
  2. 3ouj A     226 a.a. 226   X-ray 2.30 Å
  3. 2hbt A     224 a.a. 224   X-ray 1.60 Å
  4. 3hqr A     225 a.a. 224   X-ray 2.00 Å
  5. 4bqy A     221 a.a. 221   X-ray 1.53 Å
   more ...
There are no PDB entries containing vitamin c bound to this target protein, although there are 17 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 14:   UniProt id: Q9UHI7 (S23A1_HUMAN)  -  Solute carrier family 23 member 1
UniProt id: Q9UHI7    598 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: 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 16:   UniProt id: Q9H6Z9 (EGLN3_HUMAN)  -  Egl nine homolog 3
UniProt id: Q9H6Z9    239 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: 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 18:   UniProt id: Q9NXG6 (P4HTM_HUMAN)  -  Putative HIF-prolyl hydroxylase PH-4
UniProt id: Q9NXG6    502 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: Q54873 (HYSA_STRPN)  -  Hyaluronate lyase
UniProt id: Q54873    1065 a.a.  
1f9g A   721 a.a. 713   X-ray 2.00 Å
The PDB contains 1 entry of vitamin c bound to this target protein and 19 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 20:   Bacterial outer membrane
  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 21:   UniProt id: P24300 (XYLA_STRRU)  -  Xylose isomerase
UniProt id: P24300    387 a.a.  
1xid A   387 a.a. 385   X-ray 1.70 Å
The PDB contains 1 entry of vitamin c bound to this target protein and 56 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 22:   UniProt id: O00469 (PLOD2_HUMAN)  -  Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
UniProt id: O00469    737 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: O14832 (PAHX_HUMAN)  -  Phytanoyl-CoA dioxygenase, peroxisomal
UniProt id: O14832    337 a.a.  
2a1x A     253 a.a. 253   X-ray 2.50 Å
There are no PDB entries containing vitamin c bound to this target protein, although there is 1 entry of the target protein in the PDB (see above).
DrugBank nutraceutical Target 24:   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 25:   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 vitamin c 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 26:   UniProt id: P09172 (DOPO_HUMAN)  -  Dopamine beta-hydroxylase
UniProt id: P09172    617 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 vitamin c bound in the PDB

There are 11 "non-target" proteins in the PDB containing the vitamin c 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 11 proteins are listed below.

Protein 1:   UniProt id: D9J2T9 ()  -  Ribosome inactivating protein (Fragment) OS=Momordica balsamina GN=RIP PE=1 SV=1
UniProt id: D9J2T9    245 a.a.  
4jtp A   246 a.a. 245   X-ray 1.85 Å
The PDB contains 1 entry of vitamin c bound to this protein
Protein 2:   UniProt id: P00138 ()  -  Cytochrome c' OS=Alcaligenes xylosoxydans xylosoxydans PE=1 SV=2
UniProt id: P00138    126 a.a.  
1. 4cip A   125 a.a. 124   X-ray 1.22 Å
  2. 2yld A   125 a.a. 124   X-ray 1.25 Å
  3. 3zwi A   125 a.a. 124   X-ray 1.25 Å
  4. 2ylg A   125 a.a. 123   X-ray 1.05 Å
The PDB contains 4 entries of vitamin c bound to this protein
Protein 3:   UniProt id: P00431 ()  -  Cytochrome c peroxidase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CCP1 PE=1 SV=2
UniProt id: P00431    360 a.a.  
2x08 A   293 a.a. 289   X-ray 2.01 Å
The PDB contains 1 entry of vitamin c bound to this protein
Protein 4:   UniProt id: P02883 ()  -  Thaumatin-1 OS=Thaumatococcus daniellii PE=1 SV=1
UniProt id: P02883    206 a.a.  
4tvt A   207 a.a. 206   X-ray 1.20 Å
The PDB contains 1 entry of vitamin c bound to this protein
Protein 5:   UniProt id: P29736 ()  -  Myrosinase MA1 OS=Sinapis alba PE=1 SV=2
UniProt id: P29736    500 a.a.  
1. 1e71 M   499 a.a. 499   X-ray 1.50 Å
  2. 1e73 M   499 a.a. 499   X-ray 1.50 Å
  3. 1e72 M   499 a.a. 499   X-ray 1.60 Å
The PDB contains 3 entries of vitamin c bound to this protein
Protein 6:   UniProt id: P80025 ()  -  Lactoperoxidase OS=Bos taurus GN=LPO PE=1 SV=1
UniProt id: P80025    711 a.a.  
3tgy A   594 a.a. 593   X-ray 2.35 Å
The PDB contains 1 entry of vitamin c bound to this protein
Protein 7:   UniProt id: P94678 ()  -  HTH-type transcriptional regulator TsaR OS=Comamonas testosteroni GN=tsaR PE=1 SV=1
UniProt id: P94678    298 a.a.  
3fxr A,B   296 a.a. 294   X-ray 2.50 Å
The PDB contains 1 entry of vitamin c bound to this protein
Protein 8:   UniProt id: Q43758 ()  -  Ascorbate peroxidase OS=Glycine max GN=apx1 PE=1 SV=1
UniProt id: Q43758    249 a.a.  
1oaf A   250 a.a. 249   X-ray 1.40 Å
The PDB contains 1 entry of vitamin c bound to this protein
Protein 9:   UniProt id: Q8WZK8 ()  -  DyP OS=Bjerkandera adusta GN=dyp PE=1 SV=1
UniProt id: Q8WZK8    497 a.a.  
3vxi A   438 a.a. 438   X-ray 1.50 Å
The PDB contains 1 entry of vitamin c bound to this protein
Protein 10:   UniProt id: Q9A0M7 ()  -  Hyaluronidase, phage associated OS=Streptococcus pyogenes serotype M1 GN=hylP1 PE=1 SV=1
UniProt id: Q9A0M7    336 a.a.  
1. 2pk1 A   332 a.a. 331   X-ray 3.10 Å
  2. 3eka A   332 a.a. 331   X-ray 3.10 Å
The PDB contains 2 entries of vitamin c 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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