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 |
|---|---|---|---|
| 1fcx | 184 | Retinoic acid receptor gamma |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1fcx | 184 | Retinoic acid receptor gamma | / | 1.000 | |
| 1fcy | 564 | Retinoic acid receptor gamma | / | 0.754 | |
| 1exa | 394 | Retinoic acid receptor gamma | / | 0.739 | |
| 1fd0 | 254 | Retinoic acid receptor gamma | / | 0.726 | |
| 2lbd | REA | Retinoic acid receptor gamma | / | 0.682 | |
| 4dm8 | REA | Retinoic acid receptor beta | / | 0.605 | |
| 1xdk | REA | Retinoic acid receptor beta | / | 0.600 | |
| 4dm6 | TTB | Retinoic acid receptor beta | / | 0.600 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.510 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.496 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.495 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.488 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.486 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.486 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.484 | |
| 2cul | FAD | GidA-related protein | / | 0.481 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.481 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.478 | |
| 3dl9 | V2H | Vitamin D 25-hydroxylase | / | 0.477 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.477 | |
| 3up0 | D7S | aceDAF-12 | / | 0.477 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.476 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.472 | |
| 3p6p | A6B | Camphor 5-monooxygenase | 1.14.15.1 | 0.472 | |
| 4b8u | IBK | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase | 4.2.1.59 | 0.471 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.470 | |
| 2rjp | 886 | A disintegrin and metalloproteinase with thrombospondin motifs 4 | 3.4.24.82 | 0.469 | |
| 3aba | FLI | Cytochrome P450 | / | 0.469 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.469 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.468 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.467 | |
| 1qip | GNB | Lactoylglutathione lyase | 4.4.1.5 | 0.467 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.465 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.465 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 4elb | 34R | Dihydrofolate reductase | / | 0.465 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.462 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.461 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.461 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.461 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.460 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.458 | |
| 2yiu | SMA | Cytochrome b | / | 0.458 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.458 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.457 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.457 | |
| 1jra | FAD | FAD-linked sulfhydryl oxidase ERV2 | 1.8.3.2 | 0.456 | |
| 4hw3 | 19G | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.456 | |
| 1s64 | 778 | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.455 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.455 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.455 | |
| 3cxh | SMA | Cytochrome b | / | 0.455 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.454 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.453 | |
| 4gmg | NAP | Yersiniabactin biosynthetic protein YbtU | / | 0.453 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.452 | |
| 2dji | FAD | Pyruvate oxidase | / | 0.452 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.452 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 4dhy | S41 | Glucokinase | 2.7.1.2 | 0.452 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.452 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 1fel | FEN | Retinol-binding protein 4 | / | 0.451 | |
| 2nsd | 4PI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 4i3v | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.451 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.449 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.449 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.449 | |
| 4o7u | THF | Thymidylate synthase | / | 0.449 | |
| 5doz | NDP | JamJ | / | 0.449 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.448 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.448 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.448 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.448 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3nal | DBK | Calcium-transporting ATPase | / | 0.447 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.447 | |
| 4iwv | 1J9 | Glucokinase | 2.7.1.2 | 0.447 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.447 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.446 | |
| 1v5e | FAD | Pyruvate oxidase | / | 0.446 | |
| 3up3 | XCA | aceDAF-12 | / | 0.446 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.446 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.445 | |
| 2hm9 | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.445 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.445 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1fp1 | HCC | Isoliquiritigenin 2'-O-methyltransferase | / | 0.444 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.444 | |
| 3bhr | THG | Thymidylate synthase | / | 0.444 | |
| 3fmz | 2T1 | Retinol-binding protein 4 | / | 0.444 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.443 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.443 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.443 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.443 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.442 | |
| 1r38 | NAP | NAD(P)H-dependent D-xylose reductase | 1.1.1.307 | 0.442 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.442 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 6cox | S58 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.442 | |
| 1xds | DRA | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.441 | |
| 3cth | 319 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.441 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 3uwl | FOZ | Thymidylate synthase | / | 0.441 | |
| 4cx3 | HW8 | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 1kqg | HQO | Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit | / | 0.440 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.440 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.440 | |
| 3p9t | TCL | Repressor | / | 0.440 | |
| 4g31 | 0WH | Eukaryotic translation initiation factor 2-alpha kinase 3 | 2.7.11.1 | 0.440 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.440 |