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 |
|---|---|---|---|
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 1.016 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.958 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.916 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.916 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.909 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.896 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.895 | |
| 5mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.879 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.872 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.866 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.842 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.831 | |
| 2zcj | SAH | Modification methylase HhaI | 2.1.1.37 | 0.831 | |
| 8mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.830 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.813 | |
| 4dkj | SAH | Cytosine-specific methyltransferase | / | 0.786 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.768 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.765 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.756 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.751 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.741 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.737 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.734 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.732 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.730 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.730 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.730 | |
| 1wg8 | SAM | Ribosomal RNA small subunit methyltransferase H | / | 0.729 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.729 | |
| 2zif | SAM | Methyltransferase | / | 0.728 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.727 | |
| 2f8l | SAM | Lmo1582 protein | / | 0.725 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.724 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.720 | |
| 3c3y | SAH | O-methyltransferase | / | 0.720 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.720 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.719 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.718 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.718 | |
| 2zzn | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.717 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.717 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.716 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.715 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.713 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.712 | |
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 0.709 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.709 | |
| 4poo | SAM | Putative RNA methylase | / | 0.708 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.704 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.703 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.702 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.702 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.701 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.701 | |
| 4h0n | SAH | Dnmt2 | / | 0.700 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.699 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.697 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.697 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.696 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.695 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.695 | |
| 3eey | SAM | rRNA methylase | / | 0.694 | |
| 3tlj | SAH | Uncharacterized protein | / | 0.694 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.694 | |
| 5k7u | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.694 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.693 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.692 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.692 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.690 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.690 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.690 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.690 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.689 | |
| 4tm1 | FDA | KtzI | / | 0.689 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.688 | |
| 5e9w | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.688 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.687 | |
| 4rtm | SAM | DNA adenine methylase | 2.1.1.72 | 0.687 | |
| 4ymg | SAM | Putative SAM-dependent O-methyltranferase | / | 0.687 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.686 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.686 | |
| 4fzv | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.686 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.685 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.684 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.684 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.684 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.683 | |
| 1yqz | FAD | Coenzyme A disulfide reductase | / | 0.683 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.683 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.683 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.682 | |
| 2yx1 | SFG | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.682 | |
| 3cbg | SAH | O-methyltransferase | / | 0.682 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.682 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.682 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.682 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.682 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.681 | |
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.681 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.681 | |
| 4ctj | SAM | Genome polyprotein | / | 0.681 | |
| 4kwc | SAH | Methyltransferase domain family | / | 0.681 | |
| 2bm9 | SAM | Cephalosporin hydroxylase CmcI | / | 0.680 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.680 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.680 | |
| 4tlx | FDA | KtzI | / | 0.680 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.680 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.679 | |
| 4tm4 | FDA | KtzI | / | 0.678 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.677 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.675 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.675 | |
| 3lby | SAH | Uncharacterized protein | / | 0.675 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.675 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.674 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.673 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.673 | |
| 1bc5 | SAH | Chemotaxis protein methyltransferase | 2.1.1.80 | 0.672 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.671 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.671 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.671 | |
| 4kvz | SAH | PtnL protein | / | 0.671 | |
| 4pyn | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.671 | |
| 4xcx | SAH | Small RNA 2'-O-methyltransferase | / | 0.671 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.671 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.670 | |
| 1jr4 | CL4 | Catechol O-methyltransferase | 2.1.1.6 | 0.669 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.669 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.669 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.669 | |
| 4mb2 | ATP | Uncharacterized protein | / | 0.669 | |
| 4rtl | SFG | DNA adenine methylase | 2.1.1.72 | 0.669 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.669 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.668 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.668 | |
| 3axt | SAM | tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | / | 0.668 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.668 | |
| 3lst | SAH | CalO1 | / | 0.667 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.666 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.666 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.666 | |
| 1l9k | SAH | Genome polyprotein | 2.7.7.48 | 0.665 | |
| 4c05 | SAH | Protein arginine N-methyltransferase 6 | / | 0.665 | |
| 4tm3 | FAD | KtzI | / | 0.665 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.665 | |
| 3lcc | SAH | Thiocyanate methyltransferase 1 | / | 0.664 | |
| 4k6m | SAH | Genome polyprotein | / | 0.664 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.663 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.663 | |
| 3tos | SAH | CalS11 | / | 0.663 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.663 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.663 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.662 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.662 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.662 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.661 | |
| 2hnk | SAH | SAM-dependent O-methyltransferase | / | 0.660 | |
| 5il1 | SAM | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.660 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.659 | |
| 3bwc | SAM | Spermidine synthase, putative | / | 0.659 | |
| 4hh4 | SAH | CcbJ | / | 0.659 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.658 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.658 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.658 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.657 | |
| 2nxe | SAM | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.657 | |
| 2oy0 | SAH | Genome polyprotein | / | 0.657 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.657 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.657 | |
| 4uck | SAM | Large structural protein | / | 0.657 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.656 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.656 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.656 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.655 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.655 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.654 | |
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.654 | |
| 3rha | FDA | Putrescine oxidase | / | 0.654 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.653 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.652 | |
| 3lfz | ADP | Uncharacterized protein MJ1225 | / | 0.652 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.651 | |
| 1qao | SAM | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.651 | |
| 1qzz | SAM | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.651 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.651 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.651 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.651 | |
| 4yuv | S4M | Spermidine synthase, putative | / | 0.651 | |
| 1npx | FAD | NADH peroxidase | 1.11.1.1 | 0.650 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.650 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.650 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.650 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.650 | |
| 3evc | SAH | Genome polyprotein | 2.1.1.56 | 0.650 | |
| 3hvk | 719 | Catechol O-methyltransferase | 2.1.1.6 | 0.650 | |
| 4egu | 5GP | Putative histidine triad (HIT) protein | / | 0.650 |