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 |
|---|---|---|---|
| 5e7o | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5e7o | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 1.000 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.612 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.592 | |
| 4ef4 | C2E | Stimulator of interferon genes protein | / | 0.482 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.481 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.481 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.476 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.476 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.474 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.473 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.473 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.472 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.471 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.470 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.469 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.469 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.468 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.468 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.468 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.468 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.468 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.468 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.467 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.467 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.467 | |
| 4f9g | C2E | Stimulator of interferon genes protein | / | 0.467 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.466 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.466 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.466 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.465 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.465 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.464 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.464 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.464 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.464 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.464 | |
| 4lol | 1YE | Stimulator of interferon genes protein | / | 0.464 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.464 | |
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 | 0.463 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.463 | |
| 3pmy | 41L | Endothiapepsin | 3.4.23.22 | 0.463 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.463 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.463 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.462 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.461 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.461 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.461 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.461 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.461 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.461 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.460 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 2qc8 | ADP | Glutamine synthetase | 6.3.1.2 | 0.459 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.459 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.459 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.459 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.459 | |
| 1d0m | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.458 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.458 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3a37 | ADP | ATPase GET3 | / | 0.457 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.457 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.457 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.456 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.456 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.456 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.455 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.453 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.453 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.453 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.453 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.453 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.453 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.452 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.452 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.452 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.452 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.452 | |
| 2e77 | FMN | Lactate oxidase | / | 0.452 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.452 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.452 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.452 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.451 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.451 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.451 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.451 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.451 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 3u9y | 09L | Tankyrase-2 | 2.4.2.30 | 0.451 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.451 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.450 | |
| 2eka | SAH | Diphthine synthase | / | 0.450 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.450 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.450 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.450 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.450 | |
| 4blr | UTP | NTPase P4 | / | 0.450 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.450 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.449 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.449 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2b8t | THM | Thymidine kinase | / | 0.449 | |
| 3dzi | RGT | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.449 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.449 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.449 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 3w2e | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.449 | |
| 4fnc | HMU | G/T mismatch-specific thymine DNA glycosylase | 3.2.2.29 | 0.449 | |
| 4gcm | NAP | Thioredoxin reductase | 1.8.1.9 | 0.449 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.449 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.449 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.448 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.448 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.448 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.448 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.448 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.447 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.447 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.447 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.447 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.447 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.447 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.447 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.446 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.446 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.445 | |
| 1l2t | ATP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.445 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.445 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.445 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.445 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.445 | |
| 3fpj | SAM | Uncharacterized protein | / | 0.445 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.445 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.445 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.445 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.445 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.444 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.444 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3b9x | NOS | Pyrimidine-specific ribonucleoside hydrolase RihB | 3.2.2.8 | 0.444 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3ppr | 4CS | Glycine betaine/carnitine/choline-binding protein OpuCC | / | 0.444 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.444 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.444 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.443 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.443 | |
| 2p6d | SAH | Diphthine synthase | / | 0.443 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.443 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.443 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.443 | |
| 4i4b | 1CV | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.443 | |
| 4l4x | NDP | AmphI | / | 0.443 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 5dw5 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.443 | |
| 1dj2 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.442 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.442 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.442 | |
| 3gon | ANP | Phosphomevalonate kinase | / | 0.442 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.442 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.442 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.442 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.441 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.441 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.440 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4jic | FMN | GTN Reductase | / | 0.440 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.440 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 |