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 |
|---|---|---|---|
| 2hb8 | MVD | Vitamin D3 receptor |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2hb8 | MVD | Vitamin D3 receptor | / | 1.000 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.867 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.814 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.797 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.793 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.749 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.748 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.738 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.709 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.707 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.706 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.697 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.689 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.681 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.681 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.680 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.679 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.678 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.678 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.676 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.674 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.674 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.668 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.665 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.665 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.665 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.663 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.663 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.662 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.662 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.661 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.659 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.658 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.658 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.658 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.657 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.656 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.654 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.654 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.653 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.653 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.653 | |
| 2o4j | VD4 | Vitamin D3 receptor | / | 0.652 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.649 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.649 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.647 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.646 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.643 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.641 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.640 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.637 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.632 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.623 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.622 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.621 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.620 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.620 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.618 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.618 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.615 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.614 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.611 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.611 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.609 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.609 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.600 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.599 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.592 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.587 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.503 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.476 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.471 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.470 | |
| 3bej | MUF | Bile acid receptor | / | 0.469 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.466 | |
| 3cop | ADP | Glycogen synthase | 2.4.1.21 | 0.465 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.465 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.464 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.464 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.463 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.461 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.460 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.459 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.459 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.458 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.458 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.458 | |
| 4l8u | 9AZ | Serum albumin | / | 0.458 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.456 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.456 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.455 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 3up0 | D7S | aceDAF-12 | / | 0.453 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.452 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1lco | PPY | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.450 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.448 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3zep | 1NX | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.447 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.447 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.446 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.445 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.445 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.444 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.444 | |
| 3zux | TCH | Transporter | / | 0.444 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.443 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.442 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.441 | |
| 1ie4 | T44 | Transthyretin | / | 0.441 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2acw | UPG | Glycosyltransferase | / | 0.441 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.441 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.441 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.440 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.440 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.440 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.440 |