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 |
|---|---|---|---|
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 1.000 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.641 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.638 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.614 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.594 | |
| 4jv3 | N32 | Beta-ketoacyl synthase | / | 0.557 | |
| 3ho2 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.556 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.547 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.545 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.543 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.539 | |
| 2aqb | TL6 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.527 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.525 | |
| 4c6z | TLE | 3-oxoacyl-ACP synthase | / | 0.519 | |
| 2vb8 | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.515 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.506 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.487 | |
| 2wgg | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.486 | |
| 5dp2 | NAP | CurF | / | 0.482 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.481 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.474 | |
| 3cz7 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.473 | |
| 4c6u | TLG | 3-oxoacyl-ACP synthase | / | 0.471 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.470 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.470 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.469 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.468 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.467 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.467 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.467 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 3q33 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.465 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.462 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.460 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4irn | FAD | AnaB | / | 0.458 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.458 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.457 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 3i1y | 33N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.457 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.456 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.456 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.455 | |
| 3wg6 | NDP | NADPH-dependent conjugated polyketone reductase C1 | / | 0.455 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1r2j | FAD | FkbI | / | 0.454 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.454 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.453 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.453 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.453 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.453 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.452 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.452 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.451 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.451 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.451 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.451 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.450 | |
| 1c7o | PPG | Hemolysin | / | 0.449 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.449 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.449 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.449 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.448 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.448 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.448 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.448 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 3eku | CY9 | Actin-5C | / | 0.447 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.447 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.446 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.446 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3t64 | DU3 | Deoxyuridine 5'-triphosphate nucleotidohydrolase | / | 0.446 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.446 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.446 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 1opm | IYG | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.445 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.445 | |
| 3b9l | AZZ | Serum albumin | / | 0.445 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.445 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4jpe | 1M7 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.444 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.444 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.444 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.444 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.444 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.443 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.443 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2dsh | SAH | Diphthine synthase | / | 0.443 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.443 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.443 | |
| 3i28 | 34N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.443 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.442 | |
| 2zfn | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.442 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.442 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.441 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.441 | |
| 4tm1 | FDA | KtzI | / | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 2g0b | NLT | Long-chain N-acyl amino acid synthase | / | 0.440 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.440 | |
| 2ydd | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.440 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.440 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.440 |