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 |
|---|---|---|---|
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 1.000 | |
| 3ho2 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.613 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.612 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.600 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.592 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.577 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.572 | |
| 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 | 0.520 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.518 | |
| 2vb8 | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.513 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.510 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.494 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.488 | |
| 4h1q | 0XX | Matrix metalloproteinase-9 | 3.4.24.35 | 0.486 | |
| 4c6z | TLE | 3-oxoacyl-ACP synthase | / | 0.480 | |
| 4jv3 | N32 | Beta-ketoacyl synthase | / | 0.474 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.472 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.471 | |
| 5dp2 | NAP | CurF | / | 0.471 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.470 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.470 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.469 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.464 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.464 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.463 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.462 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.460 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.459 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.458 | |
| 4c6u | TLG | 3-oxoacyl-ACP synthase | / | 0.458 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.457 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.455 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.454 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.454 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.453 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.453 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.452 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.451 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.451 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.450 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.450 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.449 | |
| 3tif | ADP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.449 | |
| 4b1h | AR6 | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.449 | |
| 1l2t | ATP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.448 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.448 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.448 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.448 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.448 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.447 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.447 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.447 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.447 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.446 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.446 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.446 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.445 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.445 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4c4o | NAD | SADH | / | 0.445 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.445 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.444 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.444 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.444 | |
| 3r96 | ACO | MccE protein | / | 0.444 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.443 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.443 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.443 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.443 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.442 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.442 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.442 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.441 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.441 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.441 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 2c9b | PUG | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.440 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.440 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.440 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.440 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.440 |