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DB00170 : menadione

Approved nutraceutical menadione ... 13 targets DB00170

Generic name: menadione PDB Het Group: 17Z
 
1 structure in PDB
Brand name(s): kappaxin, kayklot, klottone, kolklot, panosine, synkavite, synkayvite.
Formula: C11H8O2
IUPAC Formula: 2-Methyl-1,4-Dihydronaphthalene-1,4-Dione
PDB name: 2-Methylnaphthalene-1,4-Diol

13
There are 13 target proteins defined in DrugBank for this nutraceutical.
 9 
9 of these target proteins have one or more structures in the PDB.
 1 
There is 1 PDB structure 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: P22891 (PROZ_HUMAN)  -  Vitamin K-dependent protein Z
UniProt id: P22891    399 a.a.  
1. 3h5c B     312 a.a. 312   X-ray 3.26 Å
  2. 3f1s B     259 a.a. 258   X-ray 2.30 Å
There are no PDB entries containing menadione 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: P16083 (NQO2_HUMAN)  -  Ribosyldihydronicotinamide dehydrogenase [quinone]
UniProt id: P16083    230 a.a.  
1. 4fgl A,B,C,D     230 a.a. 229   X-ray 1.20 Å
  2. 4fgj A,B     230 a.a. 229   X-ray 1.35 Å
  3. 4fgk A,B     230 a.a. 229   X-ray 1.40 Å
  4. 1sg0 A,B     230 a.a. 229   X-ray 1.50 Å
  5. 1xi2 A,B     230 a.a. 229   X-ray 1.50 Å
   more ...
There are no PDB entries containing menadione bound to this target protein, although there are 45 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 3:   UniProt id: P15559 (NQO1_HUMAN)  -  NAD(P)H dehydrogenase [quinone] 1
UniProt id: P15559    273 a.a.  
1. 1d4a A,B,C,D     273 a.a. 273   X-ray 1.70 Å
  2. 1kbo A,B,C,D     273 a.a. 273   X-ray 2.30 Å
  3. 1dxo A,B,C,D     273 a.a. 273   X-ray 2.50 Å
  4. 1gg5 A,B,C,D     273 a.a. 273   X-ray 2.50 Å
  5. 2f1o A,B,C,D,...     273 a.a. 273   X-ray 2.75 Å
   more ...
There are no PDB entries containing menadione 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 4:   UniProt id: P02818 (OSTCN_HUMAN)  -  Osteocalcin
UniProt id: P02818    100 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: P38435 (VKGC_HUMAN)  -  Vitamin K-dependent gamma-carboxylase
UniProt id: P38435    758 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: Q9BQB6 (VKOR1_HUMAN)  -  Vitamin K epoxide reductase complex subunit 1
UniProt id: Q9BQB6    163 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: Q8N0U8 (VKORL_HUMAN)  -  Vitamin K epoxide reductase complex subunit 1-like protein 1
UniProt id: Q8N0U8    176 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: P00734 (THRB_HUMAN)  -  Prothrombin
UniProt id: P00734    621 a.a.  
1. 4o03 A     529 a.a. 519   X-ray 3.38 Å
  2. 4nzq A     508 a.a. 508   X-ray 2.81 Å
  3. 4hzh A     392 a.a. 391   X-ray 3.30 Å
  4. 3nxp A     388 a.a. 387   X-ray 2.20 Å
  5. 1hag E     295 a.a. 295   X-ray 2.00 Å
   more ...
There are no PDB entries containing menadione bound to this target protein, although there are 354 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 9:   UniProt id: P08709 (FA7_HUMAN)  -  Coagulation factor VII
UniProt id: P08709    465 a.a.  
1. 4jze H     254 a.a. 254   X-ray 1.52 Å
  2. 2bz6 H     254 a.a. 254   X-ray 1.60 Å
  3. 2c4f H     254 a.a. 254   X-ray 1.72 Å
  4. 4jyu H     254 a.a. 254   X-ray 1.80 Å
  5. 4ish H     254 a.a. 254   X-ray 1.82 Å
   more ...
There are no PDB entries containing menadione bound to this target protein, although there are 59 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 10:   UniProt id: P00740 (FA9_HUMAN)  -  Coagulation factor IX
UniProt id: P00740    460 a.a.  
1. 3lc3 A,C     235 a.a. 235   X-ray 1.90 Å
  2. 3lc5 A     235 a.a. 235   X-ray 2.62 Å
  3. 1rfn A     235 a.a. 235   X-ray 2.80 Å
  4. 2wph E     59 a.a. 59   X-ray 1.50 Å
  5. 2wpj E     59 a.a. 59   X-ray 1.60 Å
   more ...
There are no PDB entries containing menadione bound to this target protein, although there are 16 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 11:   UniProt id: P00742 (FA10_HUMAN)  -  Coagulation factor X
UniProt id: P00742    487 a.a.  
1. 1c5m D     241 a.a. 241   X-ray 1.95 Å
  2. 1hcg A     236 a.a. 236   X-ray 2.20 Å
  3. 2xc5 A     235 a.a. 235   X-ray 1.70 Å
  4. 2xbw A     235 a.a. 235   X-ray 1.72 Å
  5. 2uwp A     235 a.a. 235   X-ray 1.75 Å
   more ...
There are no PDB entries containing menadione bound to this target protein, although there are 128 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 12:   UniProt id: P04070 (PROC_HUMAN)  -  Vitamin K-dependent protein C
UniProt id: P04070    460 a.a.  
1. 1aut C     240 a.a. 240   X-ray 2.80 Å
  2. 3f6u H     240 a.a. 240   X-ray 2.80 Å
  3. 1lqv C,D     24 a.a. 18   X-ray 1.60 Å
  4. 3jtc C,D     24 a.a. 18   X-ray 1.60 Å
There are no PDB entries containing menadione 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 13:   UniProt id: P07225 (PROS_HUMAN)  -  Vitamin K-dependent protein S
UniProt id: P07225    675 a.a.  
1z6c A     87 a.a. 87   NMR  
There are no PDB entries containing menadione 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 menadione bound in the PDB

There is 1 "non-target" protein in the PDB containing the menadione molecule bound. That is, the UniProt code for the protein is missing or does not match any of the nutraceutical targets listed above.

Protein 1:   UniProt id: I3FJN1 ()  -  Uncharacterized protein OS=Staphylococcus aureus subsp. aureus VRS4 GN=MQG_02176 PE=1 SV=1
  No Pfam domain assignments available for this protein.
4hqm A,B   99 a.a. 97   X-ray 2.55 Å
The PDB contains 1 entry of menadione bound to this protein

Key:    Secondary structure  Bound drug molecule

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

 

Structure selection

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