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 |
|---|---|---|---|
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 1.000 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.484 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.484 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.473 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.469 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.467 | |
| 4elf | 35I | Dihydrofolate reductase | / | 0.467 | |
| 3mla | JJZ | Probable nicotinate-nucleotide adenylyltransferase | / | 0.464 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.464 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.463 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.462 | |
| 4l7h | 1W1 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 5doz | NDP | JamJ | / | 0.460 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.458 | |
| 1jom | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1tw2 | ERT | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.456 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.456 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.455 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.455 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.455 | |
| 4iae | 1DX | Alr2278 protein | / | 0.455 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.454 | |
| 5dp2 | NAP | CurF | / | 0.454 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.453 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.452 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.452 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.451 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.451 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.451 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.450 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.450 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.449 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.449 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.449 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.449 | |
| 1sui | FRE | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.448 | |
| 3fow | IMH | Purine nucleoside phosphorylase | / | 0.448 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.448 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.448 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.448 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.447 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.447 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.447 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.446 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.446 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.446 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.445 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.444 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.444 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.444 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.443 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.443 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.442 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.442 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.442 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.442 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.441 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.441 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.441 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.440 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.440 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.440 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.440 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.440 |