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 |
|---|---|---|---|
| 2e82 | IM3 | D-amino-acid oxidase | 1.4.3.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2e82 | IM3 | D-amino-acid oxidase | 1.4.3.3 | 1.000 | |
| 3w4k | 3LD | D-amino-acid oxidase | 1.4.3.3 | 0.580 | |
| 3zno | SE5 | D-amino-acid oxidase | 1.4.3.3 | 0.535 | |
| 3znq | SS8 | D-amino-acid oxidase | 1.4.3.3 | 0.522 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.483 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.482 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.477 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.467 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.465 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.463 | |
| 1osv | CHC | Bile acid receptor | / | 0.461 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.461 | |
| 4y9x | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.461 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.460 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.459 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.459 | |
| 3nwl | NDP | Catalase | 1.11.1.6 | 0.459 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.458 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.457 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.457 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.456 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.454 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.454 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.453 | |
| 2ycz | I32 | Beta-1 adrenergic receptor | / | 0.453 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.452 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.452 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.452 | |
| 1odj | GMP | Purine nucleoside phosphorylase | / | 0.451 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.451 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.448 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.446 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.446 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.445 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4bgg | 844 | Activin receptor type-1 | 2.7.11.30 | 0.444 | |
| 4egn | TWO | Cytochrome P450 | / | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.444 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.444 | |
| 4myq | 19T | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4ea3 | 0NN | Nociceptin receptor | / | 0.444 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.443 | |
| 4l9q | 9TP | Serum albumin | / | 0.443 | |
| 4ple | CPS | Nuclear receptor subfamily 5 group A member 2 | / | 0.443 | |
| 1xng | DND | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.442 | |
| 2isc | 223 | Purine nucleoside phosphorylase, putative | / | 0.442 | |
| 3rj0 | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.442 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.442 | |
| 4y6n | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.442 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.441 | |
| 1tvv | CB3 | Thymidylate synthase | / | 0.441 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.441 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.440 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.440 |