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 |
|---|---|---|---|
| 1lru | BB2 | Peptide deformylase | 3.5.1.88 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1lru | BB2 | Peptide deformylase | 3.5.1.88 | 1.000 | |
| 1g2a | BB2 | Peptide deformylase | 3.5.1.88 | 0.633 | |
| 1g27 | BB1 | Peptide deformylase | 3.5.1.88 | 0.620 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.557 | |
| 3pn4 | BB2 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.532 | |
| 1ix1 | BB2 | Peptide deformylase | / | 0.502 | |
| 3m6p | BB2 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.499 | |
| 3o3j | BB4 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.499 | |
| 3u04 | BB2 | Peptide deformylase | / | 0.497 | |
| 4e9a | QAP | Peptide deformylase | / | 0.491 | |
| 2ew5 | Y12 | Peptide deformylase | / | 0.486 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.481 | |
| 1ws1 | BB2 | Peptide deformylase 1 | / | 0.479 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.474 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.466 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3e3u | NVC | Peptide deformylase | 3.5.1.88 | 0.463 | |
| 3ld6 | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.463 | |
| 5cyo | GDP | Septin-9 | / | 0.463 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.462 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.461 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.461 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.460 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.460 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.460 | |
| 3u7k | MDB | Peptide deformylase | / | 0.459 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.459 | |
| 1aj8 | COA | Citrate synthase | / | 0.458 | |
| 3zkb | ANP | DNA gyrase subunit B | / | 0.458 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.458 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.457 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.456 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.456 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.456 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.455 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.455 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.455 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.455 | |
| 4e9b | BB2 | Peptide deformylase | / | 0.455 | |
| 4h4q | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.455 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.455 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.454 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.454 | |
| 1m75 | CAA | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.453 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.453 | |
| 2o2u | 738 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.453 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.453 | |
| 5cvc | PLP | Serine racemase | / | 0.453 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.452 | |
| 2os3 | BB2 | Peptide deformylase | / | 0.452 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.452 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 1sez | OMN | Protoporphyrinogen oxidase, mitochondrial | 1.3.3.4 | 0.451 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.451 | |
| 2ejj | SAH | Diphthine synthase | / | 0.451 | |
| 2j08 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.451 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.451 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.451 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.451 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.450 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.450 | |
| 4bls | APC | NTPase P4 | / | 0.450 | |
| 4egh | 0OY | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 4lol | 1YE | Stimulator of interferon genes protein | / | 0.450 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 2ew6 | Y13 | Peptide deformylase | / | 0.449 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.449 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.449 | |
| 4qec | NAP | ElxO | / | 0.449 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.448 | |
| 1sdm | ADP | Kinesin heavy chain-like protein | / | 0.448 | |
| 1y5x | E89 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.448 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.447 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.447 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.447 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.447 | |
| 3gol | XND | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 3tjs | D0R | Cytochrome P450 3A4 | / | 0.447 | |
| 1vc2 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 4biz | ADP | Sensor histidine kinase CpxA | / | 0.446 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.446 | |
| 1lry | BB2 | Peptide deformylase | / | 0.445 | |
| 1svm | ATP | Large T antigen | 3.6.4 | 0.445 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.445 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.444 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1v1b | ATP | 2-dehydro-3-deoxygluconokinase | 2.7.1.45 | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.444 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.444 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 4fnc | HMU | G/T mismatch-specific thymine DNA glycosylase | 3.2.2.29 | 0.444 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.443 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 2bbw | GP5 | Adenylate kinase 4, mitochondrial | / | 0.443 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.443 | |
| 3upf | 0BU | Polyprotein | / | 0.443 | |
| 3uwb | BB2 | RIIA-RIIB membrane-associated protein | / | 0.443 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1ha3 | MAU | Elongation factor Tu-A | / | 0.442 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.442 | |
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.442 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 2aia | SB8 | Peptide deformylase | / | 0.442 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.442 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.442 | |
| 3sl2 | ATP | Sensor histidine kinase WalK | / | 0.442 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.442 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.442 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 4kgm | ATP | Uncharacterized protein | / | 0.441 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.441 | |
| 1o94 | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.440 | |
| 1rl4 | BRR | Peptide deformylase | / | 0.440 | |
| 2jdt | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2wq6 | FAD | RE11660p | / | 0.440 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.440 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.440 | |
| 4jld | ADP | Adenylate kinase | / | 0.440 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.440 |