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 |
|---|---|---|---|
| 2ham | C33 | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ham | C33 | Vitamin D3 receptor | / | 1.000 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.858 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.801 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.794 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.767 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.764 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.759 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.730 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.726 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.702 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.694 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.686 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.682 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.675 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.672 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.670 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.669 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.668 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.667 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.666 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.664 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.664 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.661 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.661 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.661 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.659 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.658 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.658 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.655 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.655 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.653 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.653 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.650 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.650 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.648 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.648 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.645 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.644 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.643 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.643 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.642 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.642 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.642 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.642 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.641 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.640 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.637 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.636 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.633 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.630 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.629 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.629 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.628 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.626 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.626 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.623 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.621 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.621 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.620 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.617 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.614 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.609 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.604 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.604 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.603 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.603 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.591 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.584 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.576 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.509 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.488 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.477 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.476 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.475 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.474 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.473 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.468 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.467 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.467 | |
| 3bej | MUF | Bile acid receptor | / | 0.467 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.466 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.464 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.459 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.459 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.459 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.459 | |
| 1lco | PPY | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.458 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.458 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.458 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.456 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.456 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.456 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.456 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.455 | |
| 3wd7 | COA | Acridone synthase | / | 0.455 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.454 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.454 | |
| 1eio | GCH | Gastrotropin | / | 0.453 | |
| 4h3c | 0YZ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.453 | |
| 1osv | CHC | Bile acid receptor | / | 0.452 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.451 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.451 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.451 | |
| 5ify | UMP | Glucose-1-phosphate thymidylyltransferase | / | 0.451 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.450 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.450 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.449 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.449 | |
| 1fml | RTL | Retinol dehydratase | / | 0.448 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.448 | |
| 3up0 | D7S | aceDAF-12 | / | 0.448 | |
| 1ie4 | T44 | Transthyretin | / | 0.447 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.447 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.447 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3cge | COA | Coenzyme A disulfide reductase | / | 0.447 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.447 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.446 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.446 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.446 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.446 | |
| 4l9q | 9TP | Serum albumin | / | 0.446 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.446 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.445 | |
| 1lri | CLR | Beta-elicitin cryptogein | / | 0.444 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.444 | |
| 1n4s | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.443 | |
| 1ppj | SMA | Cytochrome b | / | 0.443 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.443 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.443 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.443 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.443 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.443 | |
| 1o1v | TCH | Gastrotropin | / | 0.442 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.442 | |
| 3pgh | FLP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.442 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 4iah | 1DX | Alr2278 protein | / | 0.442 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.442 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.442 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.441 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.441 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.441 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3otq | MZL | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.441 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.441 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.440 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2go4 | TUX | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.440 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.440 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.440 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3w33 | W19 | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.440 |