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 |
|---|---|---|---|
| 4zk6 | NTM | Quinolinate synthase A |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4zk6 | NTM | Quinolinate synthase A | / | 1.000 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.490 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.483 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.483 | |
| 4l4x | NDP | AmphI | / | 0.483 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.482 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.479 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.478 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.477 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.475 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.472 | |
| 1m4i | COA | Aminoglycoside 2'-N-acetyltransferase | 2.3.1 | 0.472 | |
| 3bnk | FMN | Flavoredoxin | / | 0.472 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.470 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.470 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.467 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.467 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.466 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.466 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.465 | |
| 1ycf | FMN | Nitric oxide reductase | 1 | 0.464 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.463 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.463 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.463 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.462 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.461 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.461 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.461 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.460 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.460 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4oug | LP5 | Peptidoglycan recognition protein 1 | / | 0.460 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.459 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.459 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.459 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.459 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.459 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.458 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.457 | |
| 4brd | ANP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.457 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.456 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.456 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.456 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.455 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.455 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.455 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.455 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.455 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.455 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.455 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.455 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.455 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.455 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.454 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.454 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.454 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.454 | |
| 2h2a | DND | Probable nicotinate-nucleotide adenylyltransferase | / | 0.454 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1eje | FMN | Protein MTH_152 | / | 0.453 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.453 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.453 | |
| 2ym2 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.453 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.453 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.453 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.452 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.452 | |
| 1m9n | AMZ | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.452 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.452 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.452 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.451 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.450 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.450 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.450 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.450 | |
| 3pvc | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.450 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.450 | |
| 4d04 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 4gsu | DWZ | L,D-transpeptidase 2 | 2.3.2 | 0.450 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.449 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.449 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.449 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.449 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.449 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.449 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 1tiq | COA | Spermidine/spermine N(1)-acetyltransferase | / | 0.448 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.448 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.448 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.448 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.448 | |
| 3b05 | IPE | Isopentenyl-diphosphate delta-isomerase | / | 0.448 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.448 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.447 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.447 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.447 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.447 | |
| 2ejz | SAH | Diphthine synthase | / | 0.447 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.447 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.447 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.447 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.447 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.446 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.446 | |
| 1rx5 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.446 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.446 | |
| 3tvq | DQH | Multifunctional cyclase-dehydratase-3-O-methyl transferase TcmN | 2.1.1 | 0.446 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.446 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.446 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.445 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.445 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.445 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.445 | |
| 3w2f | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.445 | |
| 4d7m | TDC | Tetracycline repressor protein class D | / | 0.445 | |
| 4hh4 | SAH | CcbJ | / | 0.445 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.445 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.445 | |
| 5dp2 | NAP | CurF | / | 0.445 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.444 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.444 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1xgj | HTC | Beta-lactamase | 3.5.2.6 | 0.444 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.444 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.444 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.444 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.444 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.444 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.444 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.444 | |
| 4tlz | NAP | KtzI | / | 0.444 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.444 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.443 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.443 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.443 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.443 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.443 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.443 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1zpt | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.442 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.442 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 2r9w | 23C | Beta-lactamase | 3.5.2.6 | 0.442 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.442 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.442 | |
| 3int | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.442 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.442 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4j75 | TYM | Tryptophan--tRNA ligase | / | 0.442 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.442 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4q4k | FMN | Uncharacterized protein | / | 0.442 | |
| 1d4c | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.441 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.441 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.441 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.441 | |
| 2b3v | ACO | Diamine acetyltransferase 1 | / | 0.441 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.441 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.441 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 2vet | UMP | Thymidylate synthase | / | 0.441 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.441 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.441 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.441 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.441 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.441 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.440 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.440 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.440 | |
| 1sq5 | ADP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.440 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.440 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.440 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.440 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.440 | |
| 3ing | NDP | Homoserine dehydrogenase related protein | / | 0.440 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3zho | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.440 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.440 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.440 |