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 |
|---|---|---|---|
| 3gds | VAL_TYR_TYR_PHE | Serine endoprotease DegS | 3.4.21.107 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3gds | VAL_TYR_TYR_PHE | Serine endoprotease DegS | 3.4.21.107 | 1.000 | |
| 1soz | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.556 | |
| 2r3y | VAL_TYR_TRP_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.491 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.491 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.477 | |
| 4jbq | VX6 | Aurora kinase A | 2.7.11.1 | 0.476 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.473 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.473 | |
| 4rqu | NAD | Alcohol dehydrogenase class-P | / | 0.472 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.471 | |
| 4lch | 1WN | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.470 | |
| 3gcn | TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.469 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.469 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.467 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.465 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.463 | |
| 4ea3 | 0NN | Nociceptin receptor | / | 0.463 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.462 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.462 | |
| 3gco | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.461 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.461 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.460 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.460 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.459 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.459 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.459 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.458 | |
| 4aw3 | MYV | Mycinamicin IV hydroxylase/epoxidase | / | 0.458 | |
| 4l4x | NDP | AmphI | / | 0.458 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.458 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.457 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.456 | |
| 4jaq | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.456 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.455 | |
| 4s1h | ADP | Pyridoxal kinase, putative | / | 0.455 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.454 | |
| 1hf3 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 2yit | YIT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.454 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.454 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.454 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.453 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.453 | |
| 1heu | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 2nmt | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.452 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4nr4 | 2LK | CREB-binding protein | / | 0.452 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.451 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.451 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.451 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.450 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3cgo | JNO | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.450 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.450 | |
| 3uhm | RFN | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.450 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.450 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 2hfp | NSI | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.449 | |
| 3cs8 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.449 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.449 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.449 | |
| 4jap | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.449 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.449 | |
| 4px9 | ADP | ATP-dependent RNA helicase DDX3X | 3.6.4.13 | 0.449 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.448 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.448 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4b13 | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.448 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.448 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.447 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.447 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.447 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.447 | |
| 4an3 | 5Y0 | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.447 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.447 | |
| 1j3k | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.446 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.446 | |
| 4iae | 1DX | Alr2278 protein | / | 0.446 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.445 | |
| 1ppj | ANY | Cytochrome b | / | 0.445 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2j7t | 274 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.445 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.445 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.444 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.444 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.444 | |
| 3p3e | 3P3 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.444 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3t2v | KKJ | Peptidoglycan recognition protein 1 | / | 0.444 | |
| 4l9q | 9TP | Serum albumin | / | 0.444 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.444 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.444 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.443 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 4gah | 0ET | Acyl-coenzyme A thioesterase THEM4 | 3.1.2.2 | 0.443 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.443 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.442 | |
| 2yne | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.442 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3u2x | ASO | Glycogenin-1 | 2.4.1.186 | 0.442 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 4wlo | NAI | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.442 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.441 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.441 | |
| 2yir | YIR | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.441 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 3dg8 | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4iah | 1DX | Alr2278 protein | / | 0.441 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.441 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.441 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.440 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.440 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4iq7 | 1G9 | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.440 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.440 |