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 |
|---|---|---|---|
| 3bwc | SAM | Spermidine synthase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3bwc | SAM | Spermidine synthase, putative | / | 0.976 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.785 | |
| 4yv0 | S4M | Spermidine synthase, putative | / | 0.784 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.782 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.765 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.754 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.753 | |
| 5je2 | SAH | Methyl transferase | / | 0.741 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 0.737 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.736 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.731 | |
| 4kvz | SAH | PtnL protein | / | 0.730 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.726 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.722 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.721 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.720 | |
| 5fa5 | MTA | Protein arginine N-methyltransferase 5 | / | 0.720 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.719 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.718 | |
| 4gqb | 0XU | Protein arginine N-methyltransferase 5 | / | 0.713 | |
| 5je4 | SAH | Methyl transferase | / | 0.712 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.708 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.708 | |
| 5jdz | SAH | Methyl transferase | / | 0.708 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.707 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.706 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.706 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.703 | |
| 2yvl | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.703 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.701 | |
| 1ri3 | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.700 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.698 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.694 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.694 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.691 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.691 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.689 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.689 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.689 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.688 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.688 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.688 | |
| 3tos | SAH | CalS11 | / | 0.687 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.686 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.686 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.685 | |
| 3gwz | SAH | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.684 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.684 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.684 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.684 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.683 | |
| 3epp | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.683 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.682 | |
| 4oa5 | SAH | O-methyltransferase family protein | / | 0.682 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.682 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.681 | |
| 3lby | SAH | Uncharacterized protein | / | 0.680 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.679 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.678 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.676 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.676 | |
| 4tm1 | FDA | KtzI | / | 0.675 | |
| 4tm4 | FDA | KtzI | / | 0.675 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.674 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.674 | |
| 4xvy | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.674 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.673 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.672 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.671 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.671 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.670 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.670 | |
| 3iv6 | SAM | Uncharacterized protein | / | 0.670 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.669 | |
| 2xyr | SFG | Replicase polyprotein 1ab | 2.1.1 | 0.667 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.666 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.666 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.665 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.665 | |
| 3i53 | SAH | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.665 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.664 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.664 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.664 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.663 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.663 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.662 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.662 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.662 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.662 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.661 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.661 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.661 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.660 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 4d79 | ATP | tRNA threonylcarbamoyladenosine dehydratase | 6.1 | 0.658 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.658 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.657 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.657 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.656 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.656 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.655 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.655 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.655 | |
| 3p9c | SAH | Caffeic acid O-methyltransferase | / | 0.655 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.654 | |
| 4x7y | SAH | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.654 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.653 | |
| 1jq3 | AAT | Polyamine aminopropyltransferase | / | 0.652 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.652 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.652 | |
| 4e2x | SAH | Methyltransferase | / | 0.652 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.651 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.651 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.651 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.651 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.650 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.650 | |
| 4er6 | AW2 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.650 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.650 |