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 |
|---|---|---|---|
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 1.000 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.503 | |
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 0.499 | |
| 3e8s | SAH | Uncharacterized protein | / | 0.489 | |
| 5je2 | SAH | Methyl transferase | / | 0.476 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.475 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.475 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.474 | |
| 1cjw | COT | Serotonin N-acetyltransferase | / | 0.472 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.472 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.471 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.471 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.470 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.470 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.469 | |
| 1xds | DRA | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.469 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.467 | |
| 3ha7 | B32 | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.467 | |
| 3f6s | FMN | Flavodoxin | / | 0.466 | |
| 1kuv | CA5 | Serotonin N-acetyltransferase | / | 0.464 | |
| 1kux | CA3 | Serotonin N-acetyltransferase | / | 0.464 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.464 | |
| 4hh4 | SAH | CcbJ | / | 0.464 | |
| 2ewp | TXF | Estrogen-related receptor gamma | / | 0.462 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.462 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.462 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.461 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.459 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1jtq | LY3 | Thymidylate synthase | / | 0.458 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.458 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.457 | |
| 4i9i | 1DY | Tankyrase-1 | 2.4.2.30 | 0.457 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.457 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.456 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.454 | |
| 2iml | FMN | Uncharacterized protein | / | 0.453 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.453 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.453 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.453 | |
| 4rv9 | SAH | D-mycarose 3-C-methyltransferase | / | 0.453 | |
| 5dp2 | NAP | CurF | / | 0.453 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.452 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.452 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2e15 | SAH | Diphthine synthase | / | 0.452 | |
| 2pam | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.452 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.452 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.452 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.451 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.451 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.451 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.451 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.450 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.450 | |
| 3ezv | EZV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.449 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.449 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.449 | |
| 1pz0 | NAP | Protein IolS | 1.1.1 | 0.448 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.448 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.448 | |
| 2ejz | SAH | Diphthine synthase | / | 0.448 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3p9k | SAH | Caffeic acid O-methyltransferase | / | 0.448 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.448 | |
| 1xp6 | AIU | Estrogen receptor | / | 0.447 | |
| 2c2b | SAM | Threonine synthase 1, chloroplastic | 4.2.3.1 | 0.447 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.447 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.447 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.447 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.446 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 3gki | CLR | Niemann-Pick C1 protein | / | 0.446 | |
| 5doz | NDP | JamJ | / | 0.446 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.446 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.445 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.445 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.445 | |
| 1d3g | BRE | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.444 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 1ye4 | NAD | NAD(P)H-dependent D-xylose reductase | 1.1.1.307 | 0.444 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.444 | |
| 2p7z | OHT | Estrogen-related receptor gamma | / | 0.444 | |
| 3bus | SAH | Demethylrebeccamycin-D-glucose O-methyltransferase | / | 0.444 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 1fml | RTL | Retinol dehydratase | / | 0.443 | |
| 1kuy | COT | Serotonin N-acetyltransferase | / | 0.443 | |
| 1re0 | AFB | ADP-ribosylation factor 1 | / | 0.443 | |
| 1re0 | AFB | ARF guanine-nucleotide exchange factor 1 | / | 0.443 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.443 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.443 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.443 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.443 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.442 | |
| 2e08 | SAH | Diphthine synthase | / | 0.442 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.442 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.442 | |
| 3w78 | CBD | FMN-dependent NADH-azoreductase | / | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4eqw | COA | Coenzyme A disulfide reductase | / | 0.442 | |
| 4gc9 | SAM | Dimethyladenosine transferase 1, mitochondrial | 2.1.1 | 0.442 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.442 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 1tys | DHF | Thymidylate synthase | / | 0.441 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 2gd2 | CAA | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.441 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.441 | |
| 2p2x | SAH | Diphthine synthase | / | 0.441 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.441 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.441 | |
| 2xlr | NAP | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.441 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.441 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.440 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.440 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.440 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.440 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.440 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4h7c | 10H | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.440 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.440 |