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 |
|---|---|---|---|
| 2pja | 33Z | Carboxypeptidase B |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2pja | 33Z | Carboxypeptidase B | / | 1.000 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.488 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.488 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.486 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.486 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.485 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.484 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.482 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.481 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.480 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.479 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.477 | |
| 4to2 | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.477 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.473 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.473 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.471 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.470 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.469 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.469 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.468 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.468 | |
| 1req | DCA | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.467 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.467 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.467 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.467 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.465 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.465 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.465 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.464 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.463 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.463 | |
| 3qdl | FMN | Oxygen-insensitive NADPH nitroreductase | / | 0.463 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.462 | |
| 2j08 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.462 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.460 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.460 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.460 | |
| 2w0h | FAD | Trypanothione reductase | / | 0.460 | |
| 2j07 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.459 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.459 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.459 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.459 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.459 | |
| 4x5h | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.458 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3eks | CY9 | Actin-5C | / | 0.457 | |
| 3ov7 | ATP | CCA-adding enzyme | 2.7.7.72 | 0.457 | |
| 4to4 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.457 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 1pfy | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.456 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.456 | |
| 2zu8 | GDD | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.456 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.456 | |
| 4die | C5P | Cytidylate kinase | / | 0.456 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.456 | |
| 1r6t | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.455 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.455 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.455 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.455 | |
| 4l4x | NDP | AmphI | / | 0.455 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.454 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.454 | |
| 3ppr | 4CS | Glycine betaine/carnitine/choline-binding protein OpuCC | / | 0.454 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.454 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.453 | |
| 1u33 | LM2 | Pancreatic alpha-amylase | / | 0.453 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.453 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.453 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.453 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.453 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.453 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.453 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.453 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.452 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.452 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.452 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.452 | |
| 4rxq | DUT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.452 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.451 | |
| 2vtt | LZD | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.451 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.451 | |
| 4gsu | DWZ | L,D-transpeptidase 2 | 2.3.2 | 0.451 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.450 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.450 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.450 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.450 | |
| 2wca | NP6 | O-GlcNAcase BT_4395 | / | 0.450 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.450 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.450 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.449 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 2j09 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.449 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.449 | |
| 3wwm | ADP | [LysW]-aminoadipate kinase | / | 0.449 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.448 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.448 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.448 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.448 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.448 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.448 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 3nh8 | DC2 | N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming) | 3.5.1.114 | 0.448 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.448 | |
| 4dy4 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.448 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.448 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.448 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.448 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.448 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.447 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.447 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.447 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.447 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.446 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.446 | |
| 4j75 | TYM | Tryptophan--tRNA ligase | / | 0.446 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.445 | |
| 2bjh | FER | Feruloyl esterase A | 3.1.1.73 | 0.445 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.445 | |
| 2oah | QIN | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.445 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.445 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4diq | PD2 | Ribosomal oxygenase 1 | / | 0.445 | |
| 4wxf | PLG | Serine hydroxymethyltransferase | / | 0.445 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.445 | |
| 1e2n | RCA | Thymidine kinase | / | 0.444 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.444 | |
| 2fbw | CBE | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | 1.3.5.1 | 0.444 | |
| 2fbw | CBE | Succinate dehydrogenase cytochrome b, large subunit | / | 0.444 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.444 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.444 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.444 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.444 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.444 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.444 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.444 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.444 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.444 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.444 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.444 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1n1d | C2G | Glycerol-3-phosphate cytidylyltransferase | 2.7.7.39 | 0.443 | |
| 1np7 | FAD | Cryptochrome DASH | / | 0.443 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.443 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.443 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.443 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.443 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3tfn | 2CJ | Dehydrosqualene synthase | / | 0.443 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.443 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.442 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.442 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.442 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.442 | |
| 2q14 | ADP | Phosphohydrolase | / | 0.442 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.442 | |
| 3b05 | IPE | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.442 | |
| 3zho | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.442 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.442 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 4xw4 | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 5a3b | APR | SIR2 family protein | / | 0.442 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.441 | |
| 1orr | CDP | CDP-paratose 2-epimerase | / | 0.441 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.441 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.441 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.441 | |
| 2qs4 | LY5 | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.441 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.441 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3lq4 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.441 | |
| 4j7h | TRH | PCZA361.3 | / | 0.441 | |
| 4jld | ADP | Adenylate kinase | / | 0.441 | |
| 4lh7 | 1X8 | DNA ligase | / | 0.441 | |
| 4nau | AGS | Phosphopantetheine adenylyltransferase | / | 0.441 | |
| 4ohf | 5GP | Cytosolic IMP-GMP specific 5'-nucleotidase | / | 0.441 | |
| 4rxp | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.441 | |
| 6req | 3CP | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.441 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.440 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.440 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.440 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.440 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.440 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.440 |