sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 1.000 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.631 | |
| 2yoz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.630 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.629 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.608 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.572 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.570 | |
| 2ydb | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.566 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.552 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.549 | |
| 2ydd | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.519 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.498 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.497 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.492 | |
| 4wfr | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.491 | |
| 1ppj | ANY | Cytochrome b | / | 0.486 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.485 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.483 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.480 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.479 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.477 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.477 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.476 | |
| 2ylx | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.476 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.474 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.472 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.472 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.471 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.471 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.469 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.467 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.467 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.465 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.464 | |
| 3eku | CY9 | Actin-5C | / | 0.463 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.462 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.460 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.459 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.459 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.459 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.458 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.458 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.458 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.457 | |
| 2bxo | OPB | Serum albumin | / | 0.457 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.456 | |
| 1osv | CHC | Bile acid receptor | / | 0.456 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4jbs | P52 | Endoplasmic reticulum aminopeptidase 2 | 3.4.11 | 0.456 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.455 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.455 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.455 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.455 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.455 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.454 | |
| 3t88 | S0N | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.454 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.453 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.453 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.453 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.453 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 4irn | FAD | AnaB | / | 0.453 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 2aaz | CB3 | Thymidylate synthase | 2.1.1.45 | 0.452 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.452 | |
| 2wpx | ACO | Orf14 | / | 0.452 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.450 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.450 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.449 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.449 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.449 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.448 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.448 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.448 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.448 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.447 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.447 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.447 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.447 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.446 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.445 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.445 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.445 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.445 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.444 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.444 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.444 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.444 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.444 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.443 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.443 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.443 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.442 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.442 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.442 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.442 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.441 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.441 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.441 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.441 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.441 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 4fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 4fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.441 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.441 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1eio | GCH | Gastrotropin | / | 0.440 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.440 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.440 | |
| 4l9q | 9TP | Serum albumin | / | 0.440 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.440 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.440 |