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 |
|---|---|---|---|
| 1gl3 | NDP | Aspartate-semialdehyde dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1gl3 | NDP | Aspartate-semialdehyde dehydrogenase | / | 1.000 | |
| 1mb4 | NDP | Aspartate-semialdehyde dehydrogenase 1 | / | 0.520 | |
| 5bnt | NAP | Aspartate-semialdehyde dehydrogenase | 1.2.1.11 | 0.513 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.491 | |
| 3pzr | NAP | Aspartate-semialdehyde dehydrogenase 1 | / | 0.480 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.475 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.475 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.471 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.470 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.470 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.467 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 3u9e | COA | Lmo1369 protein | / | 0.467 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.466 | |
| 5cns | CDP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.465 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.462 | |
| 3a3b | RBF | Lumazine protein | / | 0.462 | |
| 3kjm | 245 | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.462 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.461 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.460 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.459 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.459 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.458 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.457 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.457 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.456 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.456 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.456 | |
| 3w23 | 3RO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.455 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.455 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.455 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.454 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.454 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.453 | |
| 3a3g | DLZ | Lumazine protein | / | 0.453 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.453 | |
| 1ha3 | MAU | Elongation factor Tu-A | / | 0.452 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.452 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.451 | |
| 2e9u | A25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.451 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.450 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.450 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1f20 | NAP | Nitric oxide synthase, brain | 1.14.13.39 | 0.449 | |
| 2uzt | SS3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 2vxo | XMP | GMP synthase [glutamine-hydrolyzing] | 6.3.5.2 | 0.449 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.449 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.449 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.449 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.449 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.448 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.448 | |
| 4hms | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.448 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.447 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.447 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.447 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.447 | |
| 5b0o | ADP | Flagellum-specific ATP synthase | 3.6.3.14 | 0.447 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.446 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.446 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.446 | |
| 4xj4 | 3AT | Cyclic GMP-AMP synthase | / | 0.446 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.445 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.445 | |
| 3gob | HXX | DdmC | / | 0.445 | |
| 3r8v | Z62 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4lhv | GDP | Ras-related protein Rab-8A | / | 0.445 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.445 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.444 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.444 | |
| 2g2z | COZ | Malonyl CoA-acyl carrier protein transacylase | 2.3.1.39 | 0.444 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.444 | |
| 3w2l | VRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.444 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.443 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.443 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.442 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.442 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.441 | |
| 3u8l | 09Q | Acetylcholine-binding protein | / | 0.441 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.440 |