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 |
|---|---|---|---|
| 3tye | XTZ | Dihydropteroate synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3tye | XTZ | Dihydropteroate synthase | / | 1.000 | |
| 2y5s | 78H | Dihydropteroate synthase | / | 0.537 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.482 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.469 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.464 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.463 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3uqd | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.461 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.460 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.460 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.460 | |
| 3sdk | P3N | Proteasome subunit beta type-5 | 3.4.25.1 | 0.459 | |
| 3sdk | P3N | Proteasome subunit beta type-6 | 3.4.25.1 | 0.459 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4ffl | ADP | Uncharacterized protein | / | 0.458 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.457 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 5cnn | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.456 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.454 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.452 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.452 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.451 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 2bxm | IMN | Serum albumin | / | 0.450 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2xvv | 9DN | Serum albumin | / | 0.449 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.449 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.449 | |
| 4yvz | 3AT | DNA integrity scanning protein DisA | / | 0.449 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.448 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.448 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.448 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.447 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.447 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.446 | |
| 4xx9 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.446 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.445 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.444 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.444 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 5cno | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.444 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.443 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.443 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.443 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 3kgc | LY7 | Glutamate receptor 2 | / | 0.443 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.442 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.442 | |
| 3oev | 3OE | Proteasome subunit beta type-5 | 3.4.25.1 | 0.442 | |
| 3oev | 3OE | Proteasome subunit beta type-6 | 3.4.25.1 | 0.442 | |
| 4u7w | NDP | MxaA | / | 0.442 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1ih8 | APC | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.441 | |
| 1yre | COA | Uncharacterized protein | / | 0.441 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.441 | |
| 2z50 | 028 | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.441 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.440 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.440 |