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 |
|---|---|---|---|
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.980 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.847 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.827 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.802 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 0.799 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.780 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.776 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.757 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.753 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.748 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.741 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.739 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.739 | |
| 4yv0 | S4M | Spermidine synthase, putative | / | 0.739 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.738 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.733 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.731 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.731 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.730 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.728 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.726 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.723 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.720 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.719 | |
| 3tos | SAH | CalS11 | / | 0.718 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.717 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.715 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.714 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.713 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.712 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.712 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.712 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.709 | |
| 3lby | SAH | Uncharacterized protein | / | 0.708 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.706 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.704 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.703 | |
| 4tlx | FDA | KtzI | / | 0.702 | |
| 4tm3 | FAD | KtzI | / | 0.701 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.700 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.700 | |
| 4tlz | FAD | KtzI | / | 0.700 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.700 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.699 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.699 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.698 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.698 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.698 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.697 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.697 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.697 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.697 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.697 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.697 | |
| 4tm1 | FDA | KtzI | / | 0.696 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.695 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.694 | |
| 4gf5 | SAH | CalS11 | / | 0.694 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.693 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.693 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.693 | |
| 5je2 | SAH | Methyl transferase | / | 0.691 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.690 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.689 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.689 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.689 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.688 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.688 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.688 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.685 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.685 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.685 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.685 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.684 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.683 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.683 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.683 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.683 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.683 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.683 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.680 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.679 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.679 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.679 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.678 | |
| 3dlc | SAM | SAM (And some other nucleotide) binding motif:Generic methyltransferase | / | 0.678 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.678 | |
| 1ptj | SND | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.677 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.677 | |
| 3c3y | SAH | O-methyltransferase | / | 0.677 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.674 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.674 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.674 | |
| 4hh4 | SAH | CcbJ | / | 0.674 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.674 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.674 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.673 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.672 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.672 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.669 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.669 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.669 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.668 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.668 | |
| 2xdo | FAD | TetX family tetracycline inactivation enzyme | / | 0.668 | |
| 3vaq | ADN | Putative adenosine kinase | / | 0.668 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.667 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.666 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.665 | |
| 3a4t | SFG | tRNA (cytosine(48)-C(5))-methyltransferase | 2.1.1 | 0.665 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.665 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.665 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.664 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.664 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.664 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.664 | |
| 4k39 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.664 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.663 | |
| 4qnv | GEK | tRNA U34 carboxymethyltransferase | / | 0.663 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.662 | |
| 3ukf | FDA | UDP-galactopyranose mutase | / | 0.662 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.662 | |
| 4fx9 | FAD | Coenzyme A disulfide reductase | 1.8.1.14 | 0.662 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.661 | |
| 1vjt | NAD | Alpha-glucosidase, putative | / | 0.661 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.661 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.661 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.661 | |
| 5jdz | SAH | Methyl transferase | / | 0.661 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.660 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.660 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.659 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.658 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.658 | |
| 3orh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.658 | |
| 4e2x | SAH | Methyltransferase | / | 0.658 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.657 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.657 | |
| 2dki | FAD | 3-hydroxybenzoate 4-monooxygenase | 1.14.13.23 | 0.656 | |
| 3lhd | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.656 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.656 | |
| 4mo2 | FDA | UDP-galactopyranose mutase | / | 0.656 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.656 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.655 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.655 | |
| 3kkj | FAD | Renalase | / | 0.655 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.655 | |
| 1jkf | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.654 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.654 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.653 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.653 | |
| 3iei | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.653 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.653 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.653 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.652 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.652 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.652 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.651 | |
| 1aqi | SAH | Modification methylase TaqI | 2.1.1.72 | 0.650 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.650 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.650 | |
| 3uq9 | TBN | Putative adenosine kinase | / | 0.650 |