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 |
|---|---|---|---|
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.925 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.819 | |
| 3gry | SAM | Probable ribosomal RNA small subunit methyltransferase A | / | 0.772 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.733 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.728 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.728 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.726 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.725 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.724 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.724 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.723 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.723 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.720 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.718 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.713 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.712 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.710 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.709 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.707 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.707 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.706 | |
| 4hh4 | SAH | CcbJ | / | 0.705 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.705 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.704 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.702 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.702 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.701 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.701 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.699 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.698 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.698 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.697 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.695 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.694 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.694 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.694 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.693 | |
| 3nwb | 659 | Catechol O-methyltransferase | 2.1.1.6 | 0.692 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.691 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.691 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.690 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.689 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.685 | |
| 4tm3 | FAD | KtzI | / | 0.685 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.684 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.684 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.683 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.682 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.682 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.681 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.680 | |
| 3lga | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.679 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.679 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.679 | |
| 4kvz | SAH | PtnL protein | / | 0.679 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.679 | |
| 3nwe | 662 | Catechol O-methyltransferase | 2.1.1.6 | 0.678 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.677 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.677 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.677 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.675 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.675 | |
| 3lhd | SAH | tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.219 | 0.675 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.674 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.674 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.674 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.674 | |
| 1zq9 | SAM | Probable dimethyladenosine transferase | / | 0.673 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.673 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.673 | |
| 5je2 | SAH | Methyl transferase | / | 0.673 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.672 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.672 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.672 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.671 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.671 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.670 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.669 | |
| 3kkj | FAD | Renalase | / | 0.669 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.668 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.668 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.667 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 4azw | SAM | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.667 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 5hxw | FAD | L-amino acid deaminase | / | 0.667 | |
| 5je3 | SAH | Methyl transferase | / | 0.667 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.666 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.666 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.666 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.666 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.665 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.665 | |
| 1khh | SAH | Guanidinoacetate N-methyltransferase | 2.1.1.2 | 0.664 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.664 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.664 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.664 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.664 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.663 | |
| 3emd | SFG | Methyltransferase | / | 0.663 | |
| 1pox | FAD | Pyruvate oxidase | 1.2.3.3 | 0.662 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.662 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.662 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.662 | |
| 4k2x | FAD | Polyketide oxygenase/hydroxylase | / | 0.662 | |
| 4tlx | FDA | KtzI | / | 0.662 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.661 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.661 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.661 | |
| 5bv3 | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.661 | |
| 1v59 | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.660 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.660 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.660 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.659 | |
| 3cbg | SAH | O-methyltransferase | / | 0.659 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.659 | |
| 3qgz | ADN | Histidine triad nucleotide-binding protein 1 | 3 | 0.659 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.659 | |
| 1tdn | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.658 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.658 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.657 | |
| 1ptj | SND | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.657 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.657 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.657 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.657 | |
| 3bus | SAH | Demethylrebeccamycin-D-glucose O-methyltransferase | / | 0.657 | |
| 1la2 | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.656 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.656 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.655 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.655 | |
| 2pwy | SAH | tRNA (adenine(58)-N(1))-methyltransferase TrmI | 2.1.1.220 | 0.655 | |
| 3n1s | 5GP | Purine nucleoside phosphoramidase | / | 0.655 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.655 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.654 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.654 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.653 | |
| 3fws | ANP | Transcriptional repressor CcpN | / | 0.653 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.652 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.652 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.650 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.650 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.650 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.650 | |
| 5jdz | SAH | Methyl transferase | / | 0.650 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.650 |