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 |
|---|---|---|---|
| 2hmv | ADP | Ktr system potassium uptake protein A |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2hmv | ADP | Ktr system potassium uptake protein A | / | 0.911 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.749 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.749 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.731 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.731 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.719 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.719 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.717 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.714 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.714 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.712 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.711 | |
| 1ahh | NAD | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.709 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.709 | |
| 1sqf | SAM | Ribosomal RNA small subunit methyltransferase B | 2.1.1.176 | 0.706 | |
| 3rw9 | DSH | Spermidine synthase | 2.5.1.16 | 0.706 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.706 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.704 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.704 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.704 | |
| 5je4 | SAH | Methyl transferase | / | 0.704 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.702 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.702 | |
| 4rtk | SAH | DNA adenine methylase | 2.1.1.72 | 0.702 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.700 | |
| 4m55 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.700 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.697 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.696 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.696 | |
| 5e72 | SAM | N2, N2-dimethylguanosine tRNA methyltransferase | / | 0.696 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.695 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.695 | |
| 2hms | NAI | Ktr system potassium uptake protein A | / | 0.695 | |
| 2vdv | SAM | tRNA (guanine-N(7)-)-methyltransferase | / | 0.695 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.695 | |
| 1eg2 | MTA | Modification methylase RsrI | 2.1.1.72 | 0.693 | |
| 4tlx | FDA | KtzI | / | 0.693 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.692 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.692 | |
| 4dcm | SAM | Ribosomal RNA large subunit methyltransferase G | 2.1.1.174 | 0.692 | |
| 5ccb | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.691 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.690 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.690 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.690 | |
| 1qaq | SFG | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.689 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.689 | |
| 4tlz | FAD | KtzI | / | 0.689 | |
| 4yv2 | S4M | Spermidine synthase, putative | / | 0.689 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.688 | |
| 2pt6 | S4M | Spermidine synthase | / | 0.687 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.685 | |
| 2zzn | SAM | tRNA (guanine(37)-N1)-methyltransferase Trm5b | 2.1.1.228 | 0.685 | |
| 2o07 | MTA | Spermidine synthase | 2.5.1.16 | 0.684 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.684 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.683 | |
| 5jdz | SAH | Methyl transferase | / | 0.683 | |
| 2dpm | SAM | Modification methylase DpnIIA | 2.1.1.72 | 0.682 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.682 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.681 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.681 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.681 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.681 | |
| 2uyh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.681 | |
| 3e9y | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.681 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.681 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.680 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.680 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.680 | |
| 1nbh | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.679 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.679 | |
| 2okc | SAM | Probable type I restriction enzyme BthVORF4518P M protein | 2.1.1.72 | 0.679 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.679 | |
| 4fp9 | SAM | 5-methylcytosine rRNA methyltransferase NSUN4 | 2.1.1 | 0.679 | |
| 4tm3 | FAD | KtzI | / | 0.679 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.678 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.678 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.678 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.678 | |
| 1uay | ADN | Oxidoreductase | / | 0.677 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.677 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.677 | |
| 4tm4 | FDA | KtzI | / | 0.677 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.676 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.676 | |
| 3ihg | FAD | Aklavinone 12-hydroxylase RdmE | / | 0.676 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.676 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.675 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.675 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.675 | |
| 4qdk | SAH | Magnesium-protoporphyrin O-methyltransferase | 2.1.1.11 | 0.675 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.674 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.674 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.674 | |
| 2nyu | SAM | rRNA methyltransferase 2, mitochondrial | / | 0.674 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.674 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.674 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.673 | |
| 4er6 | AW2 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.673 | |
| 4tm0 | FAD | KtzI | / | 0.673 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.672 | |
| 2bh2 | SAH | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | / | 0.671 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.670 | |
| 1fjx | SAH | Modification methylase HhaI | 2.1.1.37 | 0.670 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.670 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.670 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.670 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.670 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.670 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.669 | |
| 2zth | SAM | Catechol O-methyltransferase | 2.1.1.6 | 0.669 | |
| 3nmu | SAM | Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase | / | 0.669 | |
| 3tos | SAH | CalS11 | / | 0.669 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.669 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.668 | |
| 2cdu | ADP | NADH oxidase | / | 0.668 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.668 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.668 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.668 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.667 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.667 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.667 | |
| 4poo | SAM | Putative RNA methylase | / | 0.667 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.666 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.666 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.666 | |
| 4rts | SAM | DNA adenine methylase | 2.1.1.72 | 0.666 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.665 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.665 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.665 | |
| 5je2 | SAH | Methyl transferase | / | 0.665 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.664 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.664 | |
| 4yv1 | S4M | Spermidine synthase, putative | / | 0.664 | |
| 1p1h | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.663 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.663 | |
| 2ytz | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.663 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.663 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 1rjd | SAM | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.662 | |
| 3u81 | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.662 | |
| 4rtq | SAH | DNA adenine methylase | 2.1.1.72 | 0.662 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.662 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 1rjg | SAH | Leucine carboxyl methyltransferase 1 | 2.1.1.233 | 0.661 | |
| 2p35 | SAH | Trans-aconitate 2-methyltransferase | / | 0.661 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.660 | |
| 3fpf | MTA | Uncharacterized protein | / | 0.660 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.659 | |
| 2ih5 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.659 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.659 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.659 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.659 | |
| 2oy0 | SAH | Genome polyprotein | / | 0.658 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.658 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.657 | |
| 3wst | SAH | Protein arginine N-methyltransferase 7 | 2.1.1 | 0.657 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.657 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.657 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.656 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.656 | |
| 2v7g | NAD | Urocanate hydratase | 4.2.1.49 | 0.656 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.656 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.656 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.656 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.656 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.656 | |
| 1y9d | FAD | Pyruvate oxidase | 1.2.3.3 | 0.655 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.655 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.655 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.654 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.654 | |
| 2qe6 | SAM | Uncharacterized protein | / | 0.654 | |
| 5jjr | SAH | Genome polyprotein | / | 0.654 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.653 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.653 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.653 | |
| 2br5 | SAH | Cephalosporin hydroxylase CmcI | / | 0.652 | |
| 3duw | SAH | O-methyltransferase, putative | / | 0.652 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.652 | |
| 3oe4 | 610 | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 3pvz | NAD | UDP-N-acetylglucosamine 4,6-dehydratase | / | 0.652 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.652 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.652 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.652 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.651 | |
| 4c4o | NAD | SADH | / | 0.651 | |
| 4gf5 | SAH | CalS11 | / | 0.651 | |
| 4u7t | SAH | DNA (cytosine-5)-methyltransferase 3A | 2.1.1.37 | 0.651 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.650 | |
| 3lkz | SFG | Genome polyprotein | / | 0.650 | |
| 5fa8 | SAM | Ribosomal protein L11 methyltransferase, putative | / | 0.650 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.650 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.650 |