sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1mmk | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1mmk | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 1.000 | |
| 1kw0 | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.630 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.482 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.482 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.473 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.470 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.470 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.469 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.467 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.467 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.466 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.465 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.465 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.465 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.464 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.463 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.462 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.461 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.458 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.457 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.457 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.456 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.456 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.455 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.455 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.454 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.454 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.454 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.453 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.452 | |
| 1okn | STB | Carbonic anhydrase 2 | 4.2.1.1 | 0.451 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.451 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.450 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.450 | |
| 2fxu | BID | Actin, alpha skeletal muscle | / | 0.450 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.450 | |
| 3dzi | RGT | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.450 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.450 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.450 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.449 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.449 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.449 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.449 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.449 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.449 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.448 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.448 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.448 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.448 | |
| 4gtp | 7TP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.448 | |
| 1a9s | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.447 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.447 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.447 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.447 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4pzr | COA | Histone acetyltransferase p300 | / | 0.447 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.446 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.445 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.444 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.444 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.444 | |
| 3v2u | ATP | Protein GAL3 | / | 0.444 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.443 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.443 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.443 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.442 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.441 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.441 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.441 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4kl1 | PCG | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.441 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.440 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.440 | |
| 3wag | TYD | Glycosyltransferase | / | 0.440 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.440 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |