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 |
|---|---|---|---|
| 2d81 | RB3 | Poly(3-hydroxybutyrate) depolymerase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2d81 | RB3 | Poly(3-hydroxybutyrate) depolymerase | / | 1.000 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.490 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.485 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.482 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.476 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.471 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.471 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.471 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.470 | |
| 3eku | CY9 | Actin-5C | / | 0.470 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.470 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.469 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.469 | |
| 3b9x | NOS | Pyrimidine-specific ribonucleoside hydrolase RihB | 3.2.2.8 | 0.468 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.468 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.468 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.467 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.467 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.465 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.463 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.462 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.461 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.460 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.460 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.459 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.459 | |
| 2xgo | ZKD | Uncharacterized protein | / | 0.458 | |
| 2xvv | 9DN | Serum albumin | / | 0.458 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.458 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.457 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.456 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.455 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.455 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.454 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.454 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.454 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.454 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.453 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.453 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.452 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.452 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.451 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.451 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.451 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.450 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.450 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.450 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.449 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.449 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.449 | |
| 2bxq | IMN | Serum albumin | / | 0.448 | |
| 4eqs | COA | Coenzyme A disulfide reductase | / | 0.448 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.447 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.447 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.447 | |
| 4eqw | COA | Coenzyme A disulfide reductase | / | 0.447 | |
| 1q23 | FUA | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.446 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.446 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.446 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.446 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.446 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.446 | |
| 4ple | CPS | Nuclear receptor subfamily 5 group A member 2 | / | 0.446 | |
| 4ubt | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.446 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.445 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.445 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.445 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.445 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.444 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.444 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.444 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.444 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.444 | |
| 3w2e | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.444 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.444 | |
| 1c7o | PPG | Hemolysin | / | 0.443 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.443 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.443 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.443 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.442 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.442 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.442 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.442 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.442 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 2r96 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.441 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.441 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.441 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.441 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.441 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4hh4 | SAH | CcbJ | / | 0.441 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.441 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.440 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.440 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2zi5 | 3L1 | Deoxycytidine kinase | 2.7.1.74 | 0.440 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.440 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.440 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.440 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.440 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.440 |