sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4eiy | ZMA | Adenosine receptor A2a |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4eiy | ZMA | Adenosine receptor A2a | / | 1.000 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.748 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.686 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.685 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.660 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.657 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.651 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.647 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.646 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.644 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.638 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.560 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.516 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.511 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.506 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.503 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.490 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.485 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.484 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.483 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.482 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.480 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.479 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.478 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.474 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.474 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.473 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.470 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.468 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.468 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 1tw2 | ERT | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.467 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.466 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.465 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.465 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.464 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.463 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.461 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.460 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.460 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.460 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.459 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.459 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.459 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.458 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.458 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.457 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.456 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.456 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.456 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.455 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.455 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.455 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.455 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.454 | |
| 2d1c | NAP | Isocitrate dehydrogenase [NADP] | 1.1.1.42 | 0.454 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.454 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.454 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.453 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.453 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.453 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.452 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.452 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.452 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.452 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.450 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.450 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.449 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.449 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.448 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.448 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.447 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.447 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.446 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.446 | |
| 4iae | 1DX | Alr2278 protein | / | 0.446 | |
| 4iah | 1DX | Alr2278 protein | / | 0.446 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.445 | |
| 3poz | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.445 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.444 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.444 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.444 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.444 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.444 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.444 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.444 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.444 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.444 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4equ | G6I | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.444 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.441 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.441 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.441 | |
| 2c7g | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.441 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.441 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 3q7d | NPX | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.441 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.441 | |
| 4g20 | 484 | Vitamin D3 receptor A | / | 0.441 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.441 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.440 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.440 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.440 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.440 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.440 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.440 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.440 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.440 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.440 |