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 |
|---|---|---|---|
| 1rkh | VD2 | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1rkh | VD2 | Vitamin D3 receptor | / | 1.000 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.821 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.797 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.714 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.704 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.688 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.683 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.681 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.680 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.680 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.680 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.674 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.671 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.667 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.667 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.667 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.666 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.665 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.664 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.664 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.662 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.661 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.661 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.661 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.659 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.658 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.658 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.657 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.657 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.657 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.656 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.655 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.653 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.653 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.652 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.651 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.650 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.648 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.648 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.646 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.646 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.644 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.640 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.639 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.638 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.636 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.635 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.635 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.633 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.632 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.632 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.632 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.632 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.631 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.631 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.627 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.625 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.623 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.621 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.619 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.617 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.616 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.612 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.605 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.602 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.600 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.589 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.585 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.558 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.475 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.473 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.471 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.467 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.467 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.465 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.464 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.461 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.459 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.459 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.458 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.458 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.457 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.457 | |
| 4aos | NAP | Steroid monooxygenase | / | 0.456 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 3cge | COA | Coenzyme A disulfide reductase | / | 0.452 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 4iah | 1DX | Alr2278 protein | / | 0.450 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.449 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.448 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.448 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.447 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.447 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.447 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.447 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 1het | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.446 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 4l9q | 9TP | Serum albumin | / | 0.446 | |
| 2y3r | TRK | TamL | / | 0.445 | |
| 3cgd | COA | Coenzyme A disulfide reductase | / | 0.445 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.445 | |
| 4h0x | NAD | Iota toxin component Ia | / | 0.445 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.445 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.444 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.443 | |
| 4l8u | 9AZ | Serum albumin | / | 0.443 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.443 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.442 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.441 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.441 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.441 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.440 | |
| 4kne | 1CY | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.440 |