sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| 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 | Cavity 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 | / | 0.502 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.482 | |
| 3stx | BKA | Methylketone synthase I | / | 0.477 | |
| 1u28 | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.476 | |
| 4jd3 | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.476 | |
| 1ie4 | T44 | Transthyretin | / | 0.469 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.465 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.464 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.464 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.463 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.463 | |
| 3wec | AUI | Cytochrome P450 | / | 0.461 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.461 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.461 | |
| 2y03 | Y01 | Beta-1 adrenergic receptor | / | 0.460 | |
| 1ppj | SMA | Cytochrome b | / | 0.459 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.459 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.458 | |
| 4jlc | SU6 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.458 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.458 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.458 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.457 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.457 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.457 | |
| 2xvv | 9DN | Serum albumin | / | 0.457 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.457 | |
| 1kb9 | SMA | Cytochrome b | / | 0.455 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.455 | |
| 1ezv | SMA | Cytochrome b | / | 0.454 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.454 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.454 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.453 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.452 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.452 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.452 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.452 | |
| 1bq6 | COA | Chalcone synthase 2 | 2.3.1.74 | 0.451 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.451 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.451 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.451 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 4hee | 14R | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 1ot7 | IU5 | Bile acid receptor | / | 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 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.449 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.448 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.448 | |
| 4fyn | 0VE | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.448 | |
| 1lev | CLI | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.447 | |
| 1nqa | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.447 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.447 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.447 | |
| 3ics | ADP | Coenzyme A disulfide reductase | / | 0.447 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.447 | |
| 4ema | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3cx5 | SMA | Cytochrome b | / | 0.446 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.446 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.446 | |
| 3poz | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.446 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.445 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.445 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 4a4w | YFB | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.445 | |
| 4l2i | FAD | Electron transfer flavoprotein alpha/beta-subunit | / | 0.445 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.444 | |
| 3zw3 | ZW3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.444 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.443 | |
| 1zp9 | ATP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.442 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.442 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.442 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.442 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.442 | |
| 4nr4 | 2LK | CREB-binding protein | / | 0.442 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.441 | |
| 2gtk | 208 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.440 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.440 | |
| 3nal | DBK | Calcium-transporting ATPase | / | 0.440 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4h50 | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.440 | |
| 4uya | AGS | Mitogen-activated protein kinase kinase kinase 21 | 2.7.11.25 | 0.440 |