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 |
|---|---|---|---|
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 1.115 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 1.029 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.998 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.992 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.981 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.976 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.756 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.755 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.744 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.744 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.742 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.741 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.738 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.737 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.733 | |
| 3c3y | SAH | O-methyltransferase | / | 0.732 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.731 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.731 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.729 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.728 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.724 | |
| 3n1s | 5GP | Purine nucleoside phosphoramidase | / | 0.723 | |
| 3lby | SAH | Uncharacterized protein | / | 0.722 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.720 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.716 | |
| 2fjb | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.716 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.716 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.716 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.712 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.711 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.710 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.710 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.710 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.709 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.708 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.708 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.708 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.707 | |
| 2wba | FAD | Trypanothione reductase | 1.8.1.12 | 0.707 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.707 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.707 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.706 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.706 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.704 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.702 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.702 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.700 | |
| 1zk7 | FAD | Mercuric reductase | 1.16.1.1 | 0.700 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.700 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.699 | |
| 1zx9 | FAD | Mercuric reductase | 1.16.1.1 | 0.698 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.698 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.697 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.697 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.696 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.696 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.696 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.696 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.695 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.695 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.695 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.695 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.694 | |
| 4gr1 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.694 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.694 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.693 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.691 | |
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.690 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.690 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.690 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.690 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.689 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.689 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.688 | |
| 4yv0 | S4M | Spermidine synthase, putative | / | 0.688 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.687 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.686 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.685 | |
| 2bab | FAD | Putative aminooxidase | / | 0.684 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.684 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.683 | |
| 3l8k | ADP | Dihydrolipoamide dehydrogenase (PdhD-3) | / | 0.683 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.683 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.683 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.683 | |
| 2pja | 33Z | Carboxypeptidase B | / | 0.682 | |
| 4tm3 | FAD | KtzI | / | 0.682 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.681 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.681 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.681 | |
| 1gra | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.680 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.680 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.679 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.679 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.679 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.679 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.679 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.679 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.679 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.679 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.678 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.678 | |
| 1geu | FAD | Glutathione reductase | 1.8.1.7 | 0.678 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.678 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.678 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.678 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.678 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.678 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.677 | |
| 2c7g | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.676 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.676 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.676 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.676 | |
| 4kvz | SAH | PtnL protein | / | 0.676 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.675 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.675 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.675 | |
| 1rzy | 5AS | Histidine triad nucleotide-binding protein 1 | 3 | 0.674 | |
| 2h39 | ADQ | ADP-glucose phosphorylase | / | 0.674 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.673 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.673 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.673 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.673 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.672 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.672 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.671 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.671 | |
| 4guv | FAD | TetX family tetracycline inactivation enzyme | / | 0.671 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.670 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.670 | |
| 4poo | SAM | Putative RNA methylase | / | 0.670 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.669 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.669 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.668 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.668 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.667 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.667 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.667 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.667 | |
| 1gre | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.666 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.666 | |
| 2h59 | APR | NAD-dependent protein deacetylase | / | 0.666 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.666 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.666 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.666 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.666 | |
| 1bzl | FAD | Trypanothione reductase | 1.8.1.12 | 0.665 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.665 | |
| 1grg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.664 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.664 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.664 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.664 | |
| 4tm0 | FAD | KtzI | / | 0.664 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.664 | |
| 1grh | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.663 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.663 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.663 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.662 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.662 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.662 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.662 | |
| 3ihg | FAD | Aklavinone 12-hydroxylase RdmE | / | 0.662 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.662 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.661 | |
| 3qvt | NAI | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.661 | |
| 4jn9 | FAD | DepH | / | 0.661 | |
| 4y9d | NAI | C alpha-dehydrogenase | / | 0.661 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.661 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.660 | |
| 1ges | FAD | Glutathione reductase | 1.8.1.7 | 0.660 | |
| 1mo9 | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.660 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.660 | |
| 1k4q | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.659 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.659 | |
| 2ba9 | FAD | Putative aminooxidase | / | 0.659 | |
| 2bry | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.659 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.659 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.659 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.659 | |
| 3qvs | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.659 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
| 1bwc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.658 | |
| 1dnc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.658 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.658 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.658 | |
| 5fs6 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.658 | |
| 1s7g | APR | NAD-dependent protein deacylase 2 | / | 0.657 | |
| 3clt | FAD | Electron transfer flavoprotein subunit alpha | / | 0.657 | |
| 3dzi | RGT | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.657 | |
| 4jk3 | NAD | Uncharacterized protein | / | 0.657 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.657 | |
| 5ahk | FAD | Acetolactate synthase II, large subunit | / | 0.657 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.656 | |
| 1k0j | FAD | p-hydroxybenzoate hydroxylase | / | 0.656 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.656 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.656 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.656 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.656 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.656 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.656 | |
| 1jkf | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.655 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.655 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.654 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.654 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.654 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.654 | |
| 3wv7 | ADP | Hmd co-occurring protein HcgE | / | 0.654 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.653 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.653 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.653 | |
| 2py3 | ACP | Fibroblast growth factor receptor 2 | / | 0.653 | |
| 3rha | FDA | Putrescine oxidase | / | 0.653 | |
| 1uay | ADN | Oxidoreductase | / | 0.652 | |
| 3fbs | FAD | Oxidoreductase | / | 0.652 | |
| 3hvi | 619 | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 5d7q | AR6 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.652 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.651 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.651 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.651 | |
| 2yls | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.651 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.651 | |
| 4k2x | FAD | Polyketide oxygenase/hydroxylase | / | 0.651 | |
| 4x3q | SAH | SibL | / | 0.651 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.650 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.650 |