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 |
|---|---|---|---|
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2a14 | SAH | Indolethylamine N-methyltransferase | 2.1.1.49 | 1.000 | |
| 3kpj | SAH | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.513 | |
| 2bzg | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.494 | |
| 2i62 | SAH | Nicotinamide N-methyltransferase | 2.1.1.1 | 0.494 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.492 | |
| 4rv9 | SAH | D-mycarose 3-C-methyltransferase | / | 0.491 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.484 | |
| 1kph | SAH | Cyclopropane mycolic acid synthase 1 | 2.1.1.79 | 0.481 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.481 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.480 | |
| 4nec | SAH | Putative SAM-dependent methyltransferase | / | 0.480 | |
| 3bgv | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.478 | |
| 3up0 | D7S | aceDAF-12 | / | 0.477 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.476 | |
| 4r6x | SAH | Phosphoethanolamine N-methyltransferase | / | 0.476 | |
| 2vf0 | F89 | Thymidylate synthase | / | 0.475 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.475 | |
| 1jtq | LY3 | Thymidylate synthase | / | 0.474 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.474 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.474 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.473 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.472 | |
| 4eb4 | D16 | Thymidylate synthase | 2.1.1.45 | 0.470 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.469 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.469 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.469 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.467 | |
| 4at3 | LTI | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.467 | |
| 1w1r | ZEA | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.466 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.466 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.466 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.464 | |
| 3up3 | XCA | aceDAF-12 | / | 0.463 | |
| 1aiq | CB3 | Thymidylate synthase | / | 0.462 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.462 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.462 | |
| 3ou7 | SAM | SAM-dependent methyltransferase | / | 0.462 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.462 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 1jla | TNK | Gag-Pol polyprotein | 2.7.7.49 | 0.460 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.460 | |
| 3uj7 | SAM | Phosphoethanolamine N-methyltransferase | / | 0.460 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.460 | |
| 1axw | MTX | Thymidylate synthase | / | 0.459 | |
| 1db4 | 8IN | Phospholipase A2, membrane associated | / | 0.459 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.459 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.459 | |
| 4pzt | SOP | Histone acetyltransferase p300 | / | 0.459 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.458 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.458 | |
| 2r0c | FAD | Putative FAD-monooxygenase | / | 0.458 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.458 | |
| 4iv0 | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.458 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.457 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.457 | |
| 4fgz | SAH | Phosphoethanolamine N-methyltransferase | / | 0.457 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.456 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.456 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.456 | |
| 3v2w | ML5 | Sphingosine 1-phosphate receptor 1 | / | 0.456 | |
| 1yf3 | SAH | DNA adenine methylase | / | 0.455 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.455 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.455 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.455 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.454 | |
| 4cav | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.454 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.454 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.454 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.453 | |
| 1w1s | EMU | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.453 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.453 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.453 | |
| 5ccx | SAH | tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A | 2.1.1.220 | 0.453 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.452 | |
| 1xdk | REA | Retinoic acid receptor beta | / | 0.452 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 3hz1 | 37D | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.452 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.452 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.451 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.451 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.451 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.450 | |
| 2zfu | SAH | Ribosomal RNA-processing protein 8 | / | 0.450 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.450 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.449 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.449 | |
| 3tyl | AXW | Nitric oxide synthase, brain | 1.14.13.39 | 0.449 | |
| 3uj8 | SFG | Phosphoethanolamine N-methyltransferase | / | 0.449 | |
| 4ug9 | 1EW | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.449 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.449 | |
| 1tys | DHF | Thymidylate synthase | / | 0.448 | |
| 3t19 | 5MA | Gag-Pol polyprotein | 2.7.7.49 | 0.448 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.447 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.447 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.447 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4e2x | SAH | Methyltransferase | / | 0.447 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.447 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.446 | |
| 3e23 | SAM | Uncharacterized protein | / | 0.446 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.446 | |
| 4i7f | NVE | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 4mwz | SAM | Phosphoethanolamine N-methyltransferase, putative | / | 0.446 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.446 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.446 | |
| 4z9g | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.446 | |
| 1f4g | TP4 | Thymidylate synthase | / | 0.445 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.445 | |
| 3exn | ACO | Probable acetyltransferase | / | 0.445 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.445 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.445 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.445 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.445 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.445 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 3v2y | ML5 | Sphingosine 1-phosphate receptor 1 | / | 0.445 | |
| 1g93 | UPG | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.444 | |
| 1n4q | LYS_CYS_VAL_ILE_LEU | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.444 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.444 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.444 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.444 | |
| 5je2 | SAH | Methyl transferase | / | 0.444 | |
| 5je3 | SAH | Methyl transferase | / | 0.444 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.443 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.443 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.443 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.443 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4krh | SAM | Phosphoethanolamine N-methyltransferase 2 | / | 0.443 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 5icf | SAH | (S)-norcoclaurine 6-O-methyltransferase | / | 0.443 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.443 | |
| 1dna | CB3 | Thymidylate synthase | / | 0.442 | |
| 2aaz | CB3 | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 2xtb | KRM | Adenosine kinase, putative | / | 0.442 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3wsb | RWZ | Farnesyltransferase, putative | / | 0.442 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.442 | |
| 1kqg | MGD | Formate dehydrogenase, nitrate-inducible, major subunit | 1.1.5.6 | 0.441 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.441 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.441 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.441 | |
| 3dmj | GWE | Pol protein | / | 0.441 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.441 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.441 | |
| 4k5d | 1Q6 | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.440 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.440 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.440 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.440 | |
| 3dqr | JI2 | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 3ies | M24 | Luciferin 4-monooxygenase | 1.13.12.7 | 0.440 | |
| 3pd3 | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.440 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.440 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.440 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4fvz | 4KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 4g36 | SLU | Luciferin 4-monooxygenase | 1.13.12.7 | 0.440 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.440 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 |