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 Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4e2w | JHZ | Methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4e2w | JHZ | Methyltransferase | / | 1.000 | |
| 4e31 | JHZ | Methyltransferase | / | 0.787 | |
| 3ndj | JHZ | Methyltransferase | / | 0.710 | |
| 4e32 | DWN | Methyltransferase | / | 0.702 | |
| 4e2z | JHZ | Methyltransferase | / | 0.595 | |
| 4e2y | JHZ | Methyltransferase | / | 0.587 | |
| 4e2x | TYD | Methyltransferase | / | 0.566 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.541 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.522 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.504 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.471 | |
| 1jdt | MTA | Purine nucleoside phosphorylase | / | 0.470 | |
| 1jdv | ADN | Purine nucleoside phosphorylase | / | 0.469 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.464 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.464 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.458 | |
| 4hdh | ATP | Genome polyprotein | 2.7.7.48 | 0.458 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.458 | |
| 4xr9 | NAD | CalS8 | / | 0.458 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.457 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.456 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.456 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.454 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 1qpf | 858 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.452 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.452 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.452 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.452 | |
| 4xvu | ATP | ATPase GET3 | / | 0.452 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.451 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.449 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.449 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.449 | |
| 4dh0 | MR8 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.449 | |
| 1e2n | RCA | Thymidine kinase | / | 0.448 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.448 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.448 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.448 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.446 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.446 | |
| 4rp8 | ASC | Ascorbate-specific PTS system EIIC component | / | 0.446 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.443 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4drn | 0MC | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.443 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.442 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.442 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.442 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.441 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3x2w | ATP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.441 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.440 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.440 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.440 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.440 |