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 |
|---|---|---|---|
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 1.000 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.761 | |
| 3up0 | D7S | aceDAF-12 | / | 0.634 | |
| 3up3 | XCA | aceDAF-12 | / | 0.581 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.519 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.485 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.485 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.482 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.482 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.481 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.478 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.475 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.473 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.473 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.473 | |
| 1osv | CHC | Bile acid receptor | / | 0.471 | |
| 4o7u | THF | Thymidylate synthase | / | 0.470 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.470 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.467 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.465 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.464 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.464 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.463 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.463 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.462 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.462 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.462 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.461 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.459 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.459 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.458 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.457 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.457 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.457 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.457 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.457 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.456 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.456 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.456 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.456 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.456 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.456 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.456 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.455 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.455 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.455 | |
| 2b03 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.455 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.455 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.455 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.454 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.454 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.454 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.453 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.453 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.452 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 3p9t | TCL | Repressor | / | 0.452 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.451 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.451 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.451 | |
| 4l8u | 9AZ | Serum albumin | / | 0.451 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.450 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.450 | |
| 3aba | FLI | Cytochrome P450 | / | 0.449 | |
| 3bej | MUF | Bile acid receptor | / | 0.449 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.449 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.449 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.449 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.448 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.448 | |
| 3h6k | 33T | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.447 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3zkp | ERB | Erythromycin C-12 hydroxylase | 1.14.13.154 | 0.447 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.446 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 4iah | 1DX | Alr2278 protein | / | 0.446 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.445 | |
| 1tys | DHF | Thymidylate synthase | / | 0.445 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.445 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.445 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.445 | |
| 1jra | FAD | FAD-linked sulfhydryl oxidase ERV2 | 1.8.3.2 | 0.444 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.444 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.444 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.444 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.444 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.444 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.444 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.444 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2aaz | CB3 | Thymidylate synthase | 2.1.1.45 | 0.443 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1eio | GCH | Gastrotropin | / | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.442 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.442 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.442 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.442 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.442 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.441 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.441 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.441 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.441 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.440 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.440 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.440 | |
| 4a28 | ADP | Kinesin-like protein KIF11 | / | 0.440 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.440 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.440 |