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 |
|---|---|---|---|
| 3nkt | 1HN | Gentisate 1,2-dioxygenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3nkt | 1HN | Gentisate 1,2-dioxygenase | / | 1.000 | |
| 4fag | GTQ | Gentisate 1,2-dioxygenase | / | 0.618 | |
| 3nw4 | GTQ | Gentisate 1,2-dioxygenase | / | 0.615 | |
| 3nl1 | GTQ | Gentisate 1,2-dioxygenase | / | 0.591 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 1nhz | 486 | Glucocorticoid receptor | / | 0.488 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.481 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.481 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.481 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.479 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.476 | |
| 1dtp | APU | Diphtheria toxin | / | 0.475 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.475 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.474 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.473 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.473 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3qly | 55V | Uncharacterized protein | / | 0.471 | |
| 2gzl | 2AA | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.469 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.467 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.465 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.465 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 3nxo | D2B | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 4f79 | P53 | Putative phospho-beta-glucosidase | / | 0.465 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.464 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.463 | |
| 2oax | SNL | Mineralocorticoid receptor | / | 0.463 | |
| 3ipq | 965 | Oxysterols receptor LXR-alpha | / | 0.463 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.463 | |
| 1mvc | BM6 | Retinoic acid receptor RXR-alpha | / | 0.462 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4li6 | 1XO | Tankyrase-1 | 2.4.2.30 | 0.462 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.461 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.460 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.460 | |
| 2y53 | NAP | 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase | / | 0.460 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.459 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.459 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3cse | N22 | Uncharacterized protein | / | 0.457 | |
| 3kdi | A8S | Abscisic acid receptor PYL2 | / | 0.457 | |
| 3zrb | ORC | Progesterone receptor | / | 0.457 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.456 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.456 | |
| 4emy | PLP | Aminotransferase class I and II | / | 0.456 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.456 | |
| 1cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 2fyu | FDN | Cytochrome b | / | 0.455 | |
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 4iyg | 1HU | Strictosidine synthase | 4.3.3.2 | 0.454 | |
| 1u70 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.453 | |
| 3um6 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.453 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 1r2j | FAD | FkbI | / | 0.452 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.452 | |
| 2xvv | 9DN | Serum albumin | / | 0.452 | |
| 3v49 | PK0 | Androgen receptor | / | 0.452 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 4l7v | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.452 | |
| 1fkw | PUR | Adenosine deaminase | 3.5.4.4 | 0.451 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.451 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1u0h | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 1u0h | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 2fzh | DH1 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2fzj | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3ghw | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.450 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.449 | |
| 1k9s | FM2 | Purine nucleoside phosphorylase DeoD-type | / | 0.449 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.449 | |
| 1s9q | OHT | Estrogen-related receptor gamma | / | 0.449 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.449 | |
| 2vqs | BVD | Deoxynucleoside kinase | / | 0.449 | |
| 2w71 | L23 | Biotin carboxylase | 6.3.4.14 | 0.449 | |
| 2w8y | 486 | Progesterone receptor | / | 0.449 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.448 | |
| 2pir | DHT | Androgen receptor | / | 0.448 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 3rtm | RTM | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.448 | |
| 3um8 | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.447 | |
| 2piw | DHT | Androgen receptor | / | 0.447 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3qlw | N22 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 1ddt | APU | Diphtheria toxin | / | 0.446 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.446 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1qy2 | IPZ | Major urinary protein 1 | / | 0.446 | |
| 1w78 | PD8 | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.446 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3hf6 | LX0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.446 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.446 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.446 | |
| 1osv | CHC | Bile acid receptor | / | 0.445 | |
| 2i0v | 6C3 | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.445 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3gph | OID | Cytochrome P450 2E1 | 1.14.13 | 0.445 | |
| 3t0k | DCQ | Sulfide-quinone reductase | / | 0.445 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4gqe | 6KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.445 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.445 | |
| 1ove | 358 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.444 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3bqd | DAY | Glucocorticoid receptor | / | 0.444 | |
| 3nxv | D2F | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.444 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.444 | |
| 4uyg | 73B | Bromodomain-containing protein 2 | / | 0.444 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.443 | |
| 1qtq | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.443 | |
| 2gpu | OHT | Estrogen-related receptor gamma | / | 0.443 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3d90 | NOG | Progesterone receptor | / | 0.443 | |
| 3up0 | D7S | aceDAF-12 | / | 0.443 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.443 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4jau | ADP | Sensor histidine kinase | / | 0.443 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.443 | |
| 4zn7 | DES | Estrogen receptor | / | 0.443 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.443 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 2p7z | OHT | Estrogen-related receptor gamma | / | 0.442 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.442 | |
| 3eel | 53T | Uncharacterized protein | / | 0.442 | |
| 3gi2 | GHW | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.442 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.442 | |
| 4lwa | Q13 | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.442 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.441 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.441 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.441 | |
| 3i6q | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.441 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4jhi | EMU | Nodulin-13 | / | 0.441 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1xj7 | DHT | Androgen receptor | / | 0.440 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2qgt | EED | Estrogen receptor | / | 0.440 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.440 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3qj5 | 022 | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.440 |