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 |
|---|---|---|---|
| 1db1 | VDX | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1db1 | VDX | Vitamin D3 receptor | / | 1.000 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.842 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.790 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.771 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.738 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.735 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.719 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.709 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.696 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.691 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.686 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.678 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.677 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.676 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.671 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.670 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.669 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.667 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.666 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.662 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.662 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.661 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.660 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.660 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.658 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.658 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.658 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.657 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.656 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.653 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.653 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.653 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.652 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.651 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.650 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.650 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.646 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.646 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.644 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.641 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.640 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.639 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.639 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.638 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.638 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.636 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.635 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.634 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.633 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.632 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.627 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.625 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.623 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.621 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.620 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.616 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.616 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.610 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.608 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.608 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.606 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.604 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.603 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.603 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.595 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.591 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.585 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.577 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.574 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.483 | |
| 1lco | PPY | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.460 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.458 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.457 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.454 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.453 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.453 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.452 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3up0 | D7S | aceDAF-12 | / | 0.452 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.451 | |
| 4l9k | EHF | Serum albumin | / | 0.451 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.449 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.449 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.449 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 4jnc | 1LF | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.449 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.448 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.447 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.447 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.444 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.444 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.442 | |
| 2zbz | VDX | Vitamin D3 dihydroxylase | / | 0.442 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.442 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.442 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.442 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.442 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.442 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.442 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1ysx | 4EB | Serum albumin | / | 0.441 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.441 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.441 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.440 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.440 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.440 |