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 |
|---|---|---|---|
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 1.000 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.606 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.598 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.589 | |
| 3ho2 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.572 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.556 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.548 | |
| 2vb8 | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.514 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.504 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.490 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.489 | |
| 2aqb | TL6 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.489 | |
| 4jv3 | N32 | Beta-ketoacyl synthase | / | 0.486 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.484 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.484 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.479 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.476 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.476 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.475 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.474 | |
| 4c6z | TLE | 3-oxoacyl-ACP synthase | / | 0.471 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.470 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.470 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.470 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.469 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.469 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 2ejz | SAH | Diphthine synthase | / | 0.468 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.467 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.466 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.465 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.465 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.463 | |
| 2dsh | SAH | Diphthine synthase | / | 0.463 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.462 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.462 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.461 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.459 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.458 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.458 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.458 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.457 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.457 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.456 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.456 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.456 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.455 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.455 | |
| 3clx | X22 | E3 ubiquitin-protein ligase XIAP | 6.3.2 | 0.455 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.455 | |
| 4e2y | JHZ | Methyltransferase | / | 0.455 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 5dp2 | NAP | CurF | / | 0.455 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.454 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.454 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.454 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.452 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.452 | |
| 1r2j | FAD | FkbI | / | 0.451 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.451 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.451 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.451 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.451 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.451 | |
| 2g97 | DGB | Nicotinamide phosphoribosyltransferase | 2.4.2.12 | 0.450 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.450 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.450 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.450 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.450 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.450 | |
| 1c7o | PPG | Hemolysin | / | 0.449 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.449 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2p6d | SAH | Diphthine synthase | / | 0.448 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.448 | |
| 4h49 | L29 | Macrophage metalloelastase | 3.4.24.65 | 0.448 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.448 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.448 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.447 | |
| 1xdp | ATP | Polyphosphate kinase | / | 0.447 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.447 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.447 | |
| 3iaa | TYD | CalG2 | / | 0.447 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.447 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.446 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2e07 | SAH | Diphthine synthase | / | 0.446 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.446 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.446 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.446 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.445 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.445 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.445 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.444 | |
| 2ele | SAH | Diphthine synthase | / | 0.444 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.444 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.443 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.443 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.442 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.442 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.442 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.442 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.442 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.442 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.442 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.442 | |
| 1krv | 147 | Galactoside O-acetyltransferase | 2.3.1.18 | 0.441 | |
| 1opm | IYG | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.441 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.441 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4l1f | COS | Acyl-CoA dehydrogenase domain protein | / | 0.441 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.440 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.440 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.440 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.440 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.440 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.440 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4lut | DCS | Alanine racemase | / | 0.440 |