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 |
|---|---|---|---|
| 2d3m | COA | 5,7-dihydroxy-2-methylchromone synthase | 2.3.1.216 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2d3m | COA | 5,7-dihydroxy-2-methylchromone synthase | 2.3.1.216 | 1.000 | |
| 2d52 | COA | 5,7-dihydroxy-2-methylchromone synthase | 2.3.1.216 | 0.759 | |
| 1ee0 | CAA | 2-pyrone synthase | / | 0.596 | |
| 3wd7 | COA | Acridone synthase | / | 0.522 | |
| 3wxy | COA | Uncharacterized protein | / | 0.511 | |
| 3wy0 | COA | Uncharacterized protein | / | 0.494 | |
| 4jaq | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.493 | |
| 4jd3 | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.480 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.467 | |
| 1ppj | SMA | Cytochrome b | / | 0.466 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.466 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.465 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.463 | |
| 3wec | AUI | Cytochrome P450 | / | 0.461 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.460 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.459 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.458 | |
| 4a4w | YFB | Peroxisome proliferator-activated receptor gamma | / | 0.458 | |
| 1kb9 | SMA | Cytochrome b | / | 0.457 | |
| 1ezv | SMA | Cytochrome b | / | 0.456 | |
| 2y00 | Y01 | Beta-1 adrenergic receptor | / | 0.456 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.455 | |
| 4aw3 | MYV | Mycinamicin IV hydroxylase/epoxidase | / | 0.454 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.453 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.453 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.453 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 1bq6 | COA | Chalcone synthase 2 | 2.3.1.74 | 0.451 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 4l2i | FAD | Electron transfer flavoprotein alpha/beta-subunit | / | 0.451 | |
| 5br4 | NAD | Lactaldehyde reductase | 1.1.1.77 | 0.451 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.450 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.450 | |
| 2y03 | Y01 | Beta-1 adrenergic receptor | / | 0.449 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.449 | |
| 4f1s | F1S | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4h3c | 0YZ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.449 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.449 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.448 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.447 | |
| 3cx5 | SMA | Cytochrome b | / | 0.446 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 3poz | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.446 | |
| 4ez5 | 0RS | Cyclin-dependent kinase 6 | 2.7.11.22 | 0.446 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.446 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.445 | |
| 4a4v | YFD | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 5a27 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 1ffu | FAD | Carbon monoxide dehydrogenase medium chain | / | 0.444 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2y02 | Y01 | Beta-1 adrenergic receptor | / | 0.444 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.443 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.443 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.443 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.443 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.442 | |
| 4jia | 1K3 | Tyrosine-protein kinase JAK2 | / | 0.442 | |
| 5eox | ADP | Type 4 fimbrial biogenesis protein PilM | / | 0.442 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.441 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.441 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.441 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 4hee | 14R | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 4l3j | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.441 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.440 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.440 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.440 | |
| 3q8x | UD1 | Toxin zeta | / | 0.440 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.440 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.440 |