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DB00140 : riboflavin

Approved nutraceutical riboflavin ... 3 targets DB00140

Generic name: riboflavin PDB Het Group: RBF
 
25 structures in PDB
Brand name(s): aqua-flave, beflavin, beflavine, bisulase, dermadram, fiboflavin, flavaxin, flavin bb, flaxain, hsdb 817, hyflavin, hyre, lactobene, ovoflavin, ribipca, ribocrisina, riboderm, ribosyn, ribotone, ribovel, vitaflavine, vitasan b2.
Formula: C17H20N4O6
IUPAC Formula: 7,8-Dimethyl-10-[(2s,3s,4r)-2,3,4,5-Tetrahydroxypentyl]-2h,3h,4h,10h-Benzo[g]pteridine-2,4-Dione
PDB name: Riboflavin

3
There are 3 target proteins defined in DrugBank for this nutraceutical.
 3 
3 of these target proteins have one or more structures in the PDB.
 4 
There are 4 PDB structures of the nutraceutical molecule bound to its target protein.
 19 
There are 19 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: Q969G6 (RIFK_HUMAN)  -  Riboflavin kinase
UniProt id: Q969G6    154 a.a.  
1nb9 A   147 a.a. 146   X-ray 1.70 Å
The PDB contains 1 entry of riboflavin bound to this target protein and 4 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 2:   UniProt id: P0AFU8 (RISA_ECOLI)  -  Riboflavin synthase alpha chain
UniProt id: P0AFU8    212 a.a.  
1. 1hze A,B   97 a.a. 96   NMR  
  2. 1i18 A,B   97 a.a. 96   NMR  
  3. 1pkv A,B   87 a.a. 86   X-ray 2.60 Å
The PDB contains 3 entries of riboflavin bound to this target protein and 4 entries of this target protein in all (click on orange, plus icon for list).
DrugBank nutraceutical Target 3:   UniProt id: P30043 (BLVRB_HUMAN)  -  Flavin reductase
UniProt id: P30043    205 a.a.  
1. 1hdo A     205 a.a. 204   X-ray 1.15 Å
  2. 1he2 A     205 a.a. 204   X-ray 1.20 Å
  3. 1he3 A     204 a.a. 204   X-ray 1.40 Å
  4. 1he4 A     205 a.a. 204   X-ray 1.40 Å
  5. 1he5 A     205 a.a. 204   X-ray 1.50 Å
There are no PDB entries containing riboflavin bound to this target protein, although there are 5 entries of the target protein (click the orange, plus icon for a list).

Key:    PfamA domain  Secondary structure  Bound drug molecule

 

Other proteins with riboflavin bound in the PDB

There are 12 "non-target" proteins in the PDB containing the riboflavin 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 12 proteins are listed below.

Protein 1:   UniProt id: A1WUH0 ()  -  Dodecin OS=Halorhodospira halophila (strain DSM 244 / SL1) GN=Hhal_0546 PE=1 SV=1
UniProt id: A1WUH0    69 a.a.  
2vxa A,B,C,D,...   67 a.a. 67   X-ray 2.60 Å
The PDB contains 1 entry of riboflavin bound to this protein
Protein 2:   UniProt id: B0R5M0 ()  -  Dodecin OS=Halobacterium salinarum (strain ATCC 29341 / DSM 671 / R1) GN=OE_3073R PE=1 SV=1
UniProt id: B0R5M0    67 a.a.  
1. 2ccb A   64 a.a. 64   X-ray 1.65 Å
  2. 2cc8 A   64 a.a. 64   X-ray 1.90 Å
  3. 2vx9 A   63 a.a. 62   X-ray 1.65 Å
  4. 4b2k A   63 a.a. 62   X-ray 1.70 Å
  5. 4b2j A   63 a.a. 62   X-ray 1.90 Å
The PDB contains 6 entries of riboflavin bound to this protein
Protein 3:   UniProt id: C4TPG1 ()  -  Lumazine protein (Fragment) OS=Photobacterium kishitanii GN=lump PE=1 SV=1
UniProt id: C4TPG1    177 a.a.  
1. 3a35 A,B   184 a.a. 177   X-ray 1.42 Å
  2. 3a3b B   177 a.a. 170   X-ray 2.00 Å
The PDB contains 2 entries of riboflavin bound to this protein
Protein 4:   UniProt id: E5QVT2 ()  -  Riboflavin transporter RibU OS=Staphylococcus aureus (strain TCH60) GN=ribU PE=1 SV=1
UniProt id: E5QVT2    188 a.a.  
3p5n A,B   168 a.a. 168   X-ray 3.60 Å
The PDB contains 1 entry of riboflavin bound to this protein
Protein 5:   UniProt id: G8SX20 ()  -  Riboflavin synthase subunit alpha OS=Brucella abortus A13334 GN=BAA13334_I02741 PE=1 SV=1
UniProt id: G8SX20    201 a.a.  
4e0f A,B,C   200 a.a. 199   X-ray 2.85 Å
The PDB contains 1 entry of riboflavin bound to this protein
Protein 6:   UniProt id: P00323 ()  -  Flavodoxin OS=Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303) GN=DVU_2680 PE=1 SV=2
UniProt id: P00323    147 a.a.  
1bu5 A,B   147 a.a. 147   X-ray 1.83 Å
The PDB contains 1 entry of riboflavin bound to this protein
Protein 7:   UniProt id: Q06877 ()  -  Lumazine protein OS=Photobacterium leiognathi GN=lumP PE=1 SV=1
UniProt id: Q06877    185 a.a.  
3ddy A   175 a.a. 173   X-ray 2.50 Å
The PDB contains 1 entry of riboflavin bound to this protein
Protein 8:   UniProt id: Q56328 ()  -  Membrane lipoprotein TpN38(b) OS=Treponema pallidum (strain Nichols) GN=tpn38 PE=1 SV=1
UniProt id: Q56328    342 a.a.  
4iil A   314 a.a. 314   X-ray 1.30 Å
The PDB contains 1 entry of riboflavin bound to this protein
Protein 9:   UniProt id: Q5FWF9 ()  -  IGL@ protein OS=Homo sapiens GN=IGL@ PE=1 SV=1
UniProt id: Q5FWF9    231 a.a.  
2fl5 L,A,C,E   209 a.a. 190   X-ray 3.00 Å
The PDB contains 1 entry of riboflavin bound to this protein
Protein 10:   UniProt id: Q9HPW4 ()  -  Uncharacterized protein OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) GN=VNG_1446H PE=1 SV=1
UniProt id: Q9HPW4    76 a.a.  
1mog A   67 a.a. 67   X-ray 1.70 Å
The PDB contains 1 entry of riboflavin 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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