sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3ipk | PMS | Surface protein adhesin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ipk | PMS | Surface protein adhesin | / | 1.000 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 | 0.479 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.476 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.472 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.470 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.470 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.469 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.468 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.467 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.467 | |
| 2ejz | SAH | Diphthine synthase | / | 0.466 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 2xvh | NAP | Putative flavin-containing monooxygenase | / | 0.465 | |
| 2quj | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.464 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 3inr | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.462 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.461 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.460 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.460 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.460 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.457 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.457 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.457 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2emu | SAH | Diphthine synthase | / | 0.456 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.456 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.455 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.455 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.455 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.455 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.454 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.454 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.454 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.453 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.453 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.452 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.450 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.450 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.450 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.450 | |
| 2egs | SAH | Diphthine synthase | / | 0.449 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.449 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.449 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.449 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3int | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.448 | |
| 3jxe | TYM | Tryptophan--tRNA ligase | / | 0.448 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.448 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.447 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.447 | |
| 1u1c | BAU | Uridine phosphorylase | 2.4.2.3 | 0.446 | |
| 2emr | SAH | Diphthine synthase | / | 0.446 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.446 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.446 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.446 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.446 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1a8r | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.445 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.445 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.445 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 3pdn | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.445 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.444 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.444 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.444 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.444 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.443 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.443 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.443 | |
| 2vq7 | NAP | Putative flavin-containing monooxygenase | / | 0.443 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.443 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.443 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 5dp2 | NAP | CurF | / | 0.443 | |
| 1orr | CDP | CDP-paratose 2-epimerase | / | 0.442 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.442 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.442 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3wag | TYD | Glycosyltransferase | / | 0.442 | |
| 3wqu | ATP | Cell division protein FtsA | / | 0.442 | |
| 4b64 | NAP | L-ornithine N(5)-monooxygenase | / | 0.442 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.442 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.441 | |
| 1gax | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.441 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.441 | |
| 1p0h | COA | Mycothiol acetyltransferase | 2.3.1.189 | 0.441 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.441 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.441 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.441 | |
| 2huv | SAH | Diphthine synthase | / | 0.441 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 2owf | SAH | Diphthine synthase | / | 0.441 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.441 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.441 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.441 | |
| 2xlt | NA0 | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.441 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.441 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.440 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.440 | |
| 2eeq | SAH | Diphthine synthase | / | 0.440 | |
| 2ejk | SAH | Diphthine synthase | / | 0.440 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 3cow | 52H | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3o9p | MHI | Periplasmic murein peptide-binding protein | / | 0.440 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.440 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 |