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 |
|---|---|---|---|
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.911 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.886 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.880 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.871 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.867 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.847 | |
| 5jdz | SAH | Methyl transferase | / | 0.739 | |
| 5je3 | SAH | Methyl transferase | / | 0.739 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.735 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.727 | |
| 1aqi | SAH | Modification methylase TaqI | 2.1.1.72 | 0.725 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.720 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.714 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.712 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.711 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.711 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.710 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.710 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.709 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.708 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.707 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.704 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.702 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.702 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.700 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.699 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.699 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.698 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.698 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.697 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.697 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.697 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.696 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.695 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.694 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.694 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.693 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.693 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.691 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.690 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.690 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.689 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.689 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.688 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.687 | |
| 4tlx | FDA | KtzI | / | 0.686 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.685 | |
| 4tm1 | FDA | KtzI | / | 0.685 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.684 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.684 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.683 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.683 | |
| 4tlz | FAD | KtzI | / | 0.683 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.683 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.682 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.682 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.682 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.681 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.681 | |
| 4er6 | AW2 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.681 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.681 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.680 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.680 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.680 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.678 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.677 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.677 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.677 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.677 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.675 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.674 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.674 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.674 | |
| 1p1c | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.672 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.672 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.671 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.671 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.671 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.670 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.670 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.670 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.670 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.670 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.669 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.669 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.668 | |
| 4tm4 | FDA | KtzI | / | 0.668 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.667 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.667 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.667 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.667 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.666 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.666 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.665 | |
| 1pox | FAD | Pyruvate oxidase | 1.2.3.3 | 0.664 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.664 | |
| 4lwp | SAH | Arginine N-methyltransferase, putative | / | 0.664 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.664 | |
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.663 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.663 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.662 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.662 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.661 | |
| 3lcv | SAM | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.661 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.660 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.660 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.660 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.660 | |
| 4hh4 | SAH | CcbJ | / | 0.660 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.660 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.659 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.659 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.658 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.657 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.657 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.657 | |
| 4e2x | SAH | Methyltransferase | / | 0.657 | |
| 3alj | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.656 | |
| 3alm | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.656 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.656 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.655 | |
| 2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.654 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.653 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.653 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.652 | |
| 2zzm | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.652 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.652 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.652 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.652 | |
| 4u8n | FDA | UDP-galactopyranose mutase | / | 0.652 | |
| 5je2 | SAH | Methyl transferase | / | 0.652 | |
| 2r0c | FAD | Putative FAD-monooxygenase | / | 0.651 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.651 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.650 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.650 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.650 | |
| 3v8v | SAM | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.650 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.650 |