sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.510 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.272 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.229 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.224 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.116 | |
| 1kf6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 1.027 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 1.022 | |
| 4yxd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.022 | |
| 3aeb | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.016 | |
| 3ae4 | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.964 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.944 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.944 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.910 | |
| 1c0k | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.857 | |
| 1d4c | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.853 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.843 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.837 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.820 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.812 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.808 | |
| 1c0l | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.800 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.796 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.793 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.779 | |
| 3pvc | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.772 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.766 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.765 | |
| 3dgz | FAD | Thioredoxin reductase 2, mitochondrial | 1.8.1.9 | 0.762 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.756 | |
| 2zbw | FAD | Ferredoxin--NADP reductase | / | 0.754 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.753 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.739 | |
| 1ng3 | FAD | Glycine oxidase | 1.4.3.19 | 0.735 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.734 | |
| 4jn9 | FAD | DepH | / | 0.733 | |
| 2qa1 | FAD | PgaE | / | 0.732 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.721 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.721 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.721 | |
| 3ntd | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.720 | |
| 3sgl | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.720 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.719 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.718 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.714 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.714 | |
| 3nta | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.712 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.711 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.710 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.710 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.710 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.710 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.709 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.709 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.708 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.706 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.704 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.704 | |
| 3f8d | FAD | NADH oxidase/thioredoxin reductase | / | 0.703 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.703 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.703 | |
| 4up3 | FAD | Thioredoxin reductase | / | 0.703 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.702 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.702 | |
| 2r0c | FAD | Putative FAD-monooxygenase | / | 0.699 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.699 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.698 | |
| 2wes | FAD | Tryptophan 5-halogenase | / | 0.698 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.698 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.697 | |
| 2bab | FAD | Putative aminooxidase | / | 0.697 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.696 | |
| 4lii | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.696 | |
| 3znp | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.695 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.694 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.694 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.694 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.694 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.692 | |
| 4ntc | FAD | Thioredoxin reductase gliT | / | 0.692 | |
| 3nix | FAD | Flavoprotein/dehydrogenase | / | 0.690 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.690 | |
| 5fs9 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.690 | |
| 2hfo | FMN | Activator of photopigment and puc expression | / | 0.689 | |
| 3if9 | FAD | Glycine oxidase | 1.4.3.19 | 0.689 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.689 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.689 | |
| 4opd | FDA | Conserved Archaeal protein | / | 0.689 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.688 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.688 | |
| 3k30 | ADP | Histamine dehydrogenase | / | 0.688 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.688 | |
| 4bv6 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.688 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.687 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.687 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.687 | |
| 2eq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.686 | |
| 2nvk | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.686 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.686 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.686 | |
| 1bwc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.685 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.685 | |
| 5fs6 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.685 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.685 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.684 | |
| 2c3d | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.684 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.684 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.684 | |
| 3ef6 | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.684 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.684 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.684 | |
| 4z43 | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.684 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.683 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.683 | |
| 4cy8 | FDA | 2-hydroxybiphenyl-3-monooxygenase | / | 0.683 | |
| 1djn | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.682 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.682 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.682 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.682 | |
| 4o5u | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.682 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.681 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.681 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.681 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.681 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.681 | |
| 1cl0 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.680 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.680 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.680 | |
| 3c4a | FAD | Protodeoxyviolaceinate monooxygenase | 1 | 0.680 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.680 | |
| 3nyc | FAD | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.680 | |
| 4k2x | FAD | Polyketide oxygenase/hydroxylase | / | 0.680 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.680 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.680 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.679 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.679 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.679 | |
| 4nte | FAD | DepH | / | 0.679 | |
| 4o5q | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.679 | |
| 1m6i | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.678 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.678 | |
| 3mzi | FMN | Activator of photopigment and puc expression | / | 0.678 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.678 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.677 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.677 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.677 | |
| 4ocg | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.677 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.676 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.676 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.676 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.676 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.676 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.675 | |
| 2bac | FAD | Putative aminooxidase | / | 0.675 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.675 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.674 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.673 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.672 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.672 | |
| 3ept | FDA | Putative FAD-monooxygenase | / | 0.672 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.672 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.671 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.670 | |
| 2iw5 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.670 | |
| 2xdo | FAD | TetX family tetracycline inactivation enzyme | / | 0.670 | |
| 5fs8 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.670 | |
| 1grg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.668 | |
| 1grh | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.668 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.668 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.668 | |
| 3atq | FDA | Conserved Archaeal protein | / | 0.667 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.667 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.667 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.667 | |
| 4h50 | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.667 | |
| 4k5r | FAD | Oxygenase | / | 0.667 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.667 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.667 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.666 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.666 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.666 | |
| 2ar8 | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.665 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.665 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.664 | |
| 2aqj | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.664 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.664 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.664 | |
| 1o94 | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.663 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.663 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.663 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.663 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.663 | |
| 4usr | FAD | Monooxygenase | / | 0.663 | |
| 2ba9 | FAD | Putative aminooxidase | / | 0.662 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.662 | |
| 2tmd | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.662 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.662 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.662 | |
| 2whd | FAD | Thioredoxin reductase | / | 0.661 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.661 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.661 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.661 | |
| 4tm1 | FDA | KtzI | / | 0.661 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.660 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.660 | |
| 3uox | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.660 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.659 | |
| 2hfn | FMN | Activator of photopigment and puc expression | / | 0.658 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.658 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.658 | |
| 1yqz | FAD | Coenzyme A disulfide reductase | / | 0.657 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.656 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.655 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.655 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.654 | |
| 1gre | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.654 | |
| 3gd3 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.654 | |
| 3ka7 | FAD | Putative oxidoreductase | / | 0.654 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.654 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.653 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.653 | |
| 4hj4 | FMN | LOV protein | / | 0.653 | |
| 4jnq | FDA | Thioredoxin reductase | / | 0.653 | |
| 4z44 | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.653 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.652 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.652 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.652 | |
| 4h4s | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.652 | |
| 4ykg | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.652 | |
| 4y7c | FAD | NADPH--cytochrome P450 reductase | / | 0.651 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.651 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.650 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.650 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.650 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.650 | |
| 4eqr | FAD | Coenzyme A disulfide reductase | / | 0.650 |