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 |
|---|---|---|---|
| 4erf | 0R3 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4erf | 0R3 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 1.000 | |
| 4jvr | 1MT | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.556 | |
| 4jwr | 1MY | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.514 | |
| 4dij | BLF | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.513 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.492 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.485 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.483 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.479 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.479 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.478 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.478 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.475 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.472 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 1rv1 | IMZ | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.470 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 4ejg | NCT | Cytochrome P450 2A13 | 1.14.14.1 | 0.470 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.468 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.466 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.465 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.464 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.460 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.459 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.457 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3b9l | AZZ | Serum albumin | / | 0.454 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.454 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.454 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.453 | |
| 2w8y | 486 | Progesterone receptor | / | 0.453 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.453 | |
| 3r37 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.453 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.452 | |
| 4ere | 0R2 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.452 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.452 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.451 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.451 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.450 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.449 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3a20 | FMN | FMN-binding protein | / | 0.449 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4jsc | 1OY | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.449 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.448 | |
| 4c9o | CAM | Cytochrome P450 | / | 0.448 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.448 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.447 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.446 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.445 | |
| 3ant | S82 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.445 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.445 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.444 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.444 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.443 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.443 | |
| 1t4e | DIZ | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.443 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.443 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.443 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3dg8 | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3rmf | 20Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4em9 | TCE | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4y6g | F6F | Tryptophan synthase alpha chain | / | 0.442 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.441 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.440 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 |