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 |
|---|---|---|---|
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 1.000 | |
| 1i6x | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.540 | |
| 1i5z | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.527 | |
| 2oz6 | CMP | Cyclic AMP receptor-like protein | / | 0.517 | |
| 3n4m | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.515 | |
| 1hw5 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.513 | |
| 4i09 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.503 | |
| 4i0b | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.496 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.484 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.484 | |
| 3ryp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.484 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.481 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.478 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.478 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.474 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.473 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.467 | |
| 1rw8 | 580 | TGF-beta receptor type-1 | 2.7.11.30 | 0.466 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.465 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.465 | |
| 3zux | TCH | Transporter | / | 0.464 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.463 | |
| 3ryr | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.463 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.462 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.462 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.462 | |
| 4i0a | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.461 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.460 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.459 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.459 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.459 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.459 | |
| 4i01 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.459 | |
| 1u2d | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.458 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.458 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.458 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 4hzf | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.456 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.455 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.454 | |
| 3k3b | ADP | Kinesin-like protein KIF11 | / | 0.454 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.454 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.453 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.453 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3zew | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.453 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.452 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.452 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.452 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.451 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.451 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.451 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.450 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.450 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.450 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.449 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.449 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.449 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.448 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.448 | |
| 2oby | NAP | Quinone oxidoreductase PIG3 | 1 | 0.448 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.448 | |
| 1okk | GCP | Signal recognition particle protein | / | 0.447 | |
| 1okk | GCP | Signal recognition particle receptor FtsY | / | 0.447 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.447 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.447 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.446 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.446 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.446 | |
| 4nfh | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.446 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.445 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.445 | |
| 3nxe | 2NC | Protease | / | 0.445 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.445 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.445 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.445 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.445 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.444 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 2xyu | Q9G | Ephrin type-A receptor 4 | 2.7.10.1 | 0.444 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.443 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.443 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.442 | |
| 2gzw | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.442 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.442 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.442 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.442 | |
| 4k33 | ACP | Fibroblast growth factor receptor 3 | 2.7.10.1 | 0.442 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.441 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.441 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.441 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4fdp | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.441 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.441 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.441 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4aa4 | QC0 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4aac | AAV | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.440 |