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 |
|---|---|---|---|
| 3neg | PYV | Abscisic acid receptor PYL1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 1.000 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.564 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.555 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.542 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.533 | |
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.527 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.526 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.523 | |
| 3nef | PYV | Abscisic acid receptor PYL1 | / | 0.522 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.518 | |
| 3k3k | A8S | Abscisic acid receptor PYR1 | / | 0.516 | |
| 3r6p | A8S | Abscisic acid receptor PYL10 | / | 0.514 | |
| 3nmn | PYV | Abscisic acid receptor PYL1 | / | 0.507 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.506 | |
| 4lg5 | A1O | Abscisic acid receptor PYL2 | / | 0.498 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.493 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.492 | |
| 4oic | A8S | Bet v I allergen-like | / | 0.492 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.485 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.483 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.483 | |
| 3k90 | A8S | Abscisic acid receptor PYR1 | / | 0.479 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.479 | |
| 2acw | UPG | Glycosyltransferase | / | 0.477 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.477 | |
| 3kb3 | A8S | Abscisic acid receptor PYL2 | / | 0.475 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.471 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.467 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.466 | |
| 1yho | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.463 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.462 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.462 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 3cse | N22 | Uncharacterized protein | / | 0.460 | |
| 3eek | 53S | Uncharacterized protein | / | 0.460 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.460 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 1m8h | 6NI | Nitric oxide synthase, inducible | 1.14.13.39 | 0.458 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.458 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.458 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.457 | |
| 1s9q | OHT | Estrogen-related receptor gamma | / | 0.457 | |
| 2ze2 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.457 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.456 | |
| 4jvl | EST | Estrogen sulfotransferase | 2.8.2.4 | 0.456 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.455 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.455 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.455 | |
| 1m79 | MQ1 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1osv | CHC | Bile acid receptor | / | 0.454 | |
| 4bqg | 50Q | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 1aoe | GW3 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.453 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.452 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.452 | |
| 2cjm | ATP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.452 | |
| 2qgt | EED | Estrogen receptor | / | 0.452 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 4dk5 | 0KO | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.452 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.451 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4l23 | X6K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.451 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.450 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.450 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.450 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.450 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.450 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.449 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.448 | |
| 3kdj | A8S | Abscisic acid receptor PYL1 | / | 0.448 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.448 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.447 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4egn | TWO | Cytochrome P450 | / | 0.447 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.447 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.447 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.446 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.446 | |
| 1tkz | H16 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.446 | |
| 3q2m | CKI | Spectinomycin phosphotransferase | / | 0.446 | |
| 4a9e | 3PF | Bromodomain-containing protein 2 | / | 0.446 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 1fpq | SAM | Isoliquiritigenin 2'-O-methyltransferase | / | 0.445 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.445 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.445 | |
| 3dpd | 41A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.445 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.444 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.444 | |
| 4fa6 | 0TA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.444 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1kyo | SMA | Cytochrome b | / | 0.443 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.443 | |
| 2x7g | PVB | SRSF protein kinase 2 | 2.7.11.1 | 0.443 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.443 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.443 | |
| 3qai | XNN | Ketohexokinase | / | 0.443 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.443 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.443 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.443 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.443 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1m78 | CLZ | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2qe4 | JJ3 | Estrogen receptor | / | 0.442 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.442 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.442 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.442 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.442 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.441 | |
| 3cz0 | 9OD | Pheromone-binding protein ASP1 | / | 0.441 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3jwm | 5WB | Dihydrofolate reductase | / | 0.441 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.441 | |
| 4k5y | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.441 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.440 | |
| 2x1z | PID | Peridinin-chlorophyll a-binding protein 1, chloroplastic | / | 0.440 | |
| 3eel | 53T | Uncharacterized protein | / | 0.440 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.440 |