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 |
|---|---|---|---|
| 3w0c | 6DS | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3w0c | 6DS | Vitamin D3 receptor | / | 1.000 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.781 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.777 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.707 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.705 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.696 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.694 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.680 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.671 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.666 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.665 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.664 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.664 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.663 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.659 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.652 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.651 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.649 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.648 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.647 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.646 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.645 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.640 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.638 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.637 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.636 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.632 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.632 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.632 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.631 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.631 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.631 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.630 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.628 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.626 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.625 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.625 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.624 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.623 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.622 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.621 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.620 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.619 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.618 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.617 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.616 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.615 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.614 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.611 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.610 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.608 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.608 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.605 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.601 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.598 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.597 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.597 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.595 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.591 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.589 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.589 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.589 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.586 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.579 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.575 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.569 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.555 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.555 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.552 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.531 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.525 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.483 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.472 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.470 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.468 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 1n4s | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.459 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.459 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.455 | |
| 4l8u | 9AZ | Serum albumin | / | 0.455 | |
| 4iae | 1DX | Alr2278 protein | / | 0.453 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.451 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.450 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.447 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.447 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.447 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.446 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1osv | CHC | Bile acid receptor | / | 0.446 | |
| 3beg | ANP | SRSF protein kinase 1 | 2.7.11.1 | 0.446 | |
| 1s64 | 778 | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.445 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.445 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.443 | |
| 3bej | MUF | Bile acid receptor | / | 0.443 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.443 | |
| 1lco | PPY | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.442 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.442 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.441 | |
| 3cgc | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 3iup | NDP | Possible NADH oxidoreductase | / | 0.441 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3cx4 | ADP | Glycogen synthase | 2.4.1.21 | 0.440 | |
| 3p3e | 3P3 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.440 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.440 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.440 |