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 |
|---|---|---|---|
| 1rdt | L79 | Retinoic acid receptor RXR-alpha |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 1.000 | |
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 0.609 | |
| 2p1v | 5TN | Retinoic acid receptor RXR-alpha | / | 0.599 | |
| 1k74 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.597 | |
| 2p1t | 3TN | Retinoic acid receptor RXR-alpha | / | 0.587 | |
| 2p1u | 4TN | Retinoic acid receptor RXR-alpha | / | 0.582 | |
| 1fm9 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.581 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.580 | |
| 1fby | REA | Retinoic acid receptor RXR-alpha | / | 0.577 | |
| 1xls | REA | Retinoic acid receptor RXR-alpha | / | 0.574 | |
| 4m8h | R4M | Retinoic acid receptor RXR-alpha | / | 0.569 | |
| 3fal | REA | Retinoic acid receptor RXR-alpha | / | 0.562 | |
| 1uhl | MEI | Retinoic acid receptor RXR-beta | / | 0.561 | |
| 1xiu | REA | Retinoic acid receptor RXR | / | 0.560 | |
| 4k4j | 1O8 | Retinoic acid receptor RXR-alpha | / | 0.560 | |
| 1mvc | BM6 | Retinoic acid receptor RXR-alpha | / | 0.558 | |
| 3fc6 | REA | Retinoic acid receptor RXR-alpha | / | 0.553 | |
| 3oap | REA | Retinoic acid receptor RXR-alpha | / | 0.551 | |
| 3h0a | 9RA | Retinoic acid receptor RXR-alpha | / | 0.548 | |
| 2acl | REA | Retinoic acid receptor RXR-alpha | / | 0.547 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.546 | |
| 4m8e | 29V | Retinoic acid receptor RXR-alpha | / | 0.541 | |
| 4k6i | 9RA | Retinoic acid receptor RXR-alpha | / | 0.540 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.490 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.483 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.480 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.475 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.474 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.471 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.470 | |
| 1kk4 | ACO | Streptogramin A acetyltransferase | 2.3.1 | 0.469 | |
| 4apu | A2K | Progesterone receptor | / | 0.469 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.469 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.468 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.466 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.466 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.466 | |
| 1khr | COA | Streptogramin A acetyltransferase | 2.3.1 | 0.465 | |
| 1osv | CHC | Bile acid receptor | / | 0.465 | |
| 2cdu | FAD | NADH oxidase | / | 0.465 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.465 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.465 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.464 | |
| 3t8x | T8X | T-cell surface glycoprotein CD1b | / | 0.464 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.463 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.461 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.461 | |
| 2p15 | EZT | Estrogen receptor | / | 0.461 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.461 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.461 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.461 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.460 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.460 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.460 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.459 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.459 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.459 | |
| 3i1f | GCP | Translation initiation factor 2 subunit gamma | / | 0.459 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.459 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.459 | |
| 2e9c | B75 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.458 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.458 | |
| 4l8u | 9AZ | Serum albumin | / | 0.458 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.458 | |
| 5ab6 | CAA | Nonspecific lipid-transfer protein, putative | / | 0.458 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.457 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.457 | |
| 3p9t | TCL | Repressor | / | 0.457 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 2ewp | TXF | Estrogen-related receptor gamma | / | 0.456 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.456 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3rfm | CFF | Adenosine receptor A2a | / | 0.456 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.455 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.455 | |
| 5ab7 | MLC | Nonspecific lipid-transfer protein, putative | / | 0.455 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.455 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.454 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.454 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.454 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.454 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.453 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.453 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.453 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 1pp9 | SMA | Cytochrome b | / | 0.452 | |
| 2dqs | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.452 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3p6p | A6B | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.452 | |
| 4iw8 | KN3 | Estrogen receptor | / | 0.452 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.452 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.452 | |
| 2agv | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.451 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.451 | |
| 3aba | FLI | Cytochrome P450 | / | 0.451 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.451 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.451 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.450 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.450 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.450 | |
| 1e7a | PFL | Serum albumin | / | 0.449 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.449 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2apg | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.449 | |
| 2e99 | B08 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.449 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.449 | |
| 3nxu | RIT | Cytochrome P450 3A4 | / | 0.449 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.449 | |
| 3rpn | GTX | Glutathione S-transferase kappa 1 | 2.5.1.18 | 0.449 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.449 | |
| 1ezf | IN0 | Squalene synthase | 2.5.1.21 | 0.448 | |
| 3ar7 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.448 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.448 | |
| 3h0s | B38 | Acetyl-CoA carboxylase | / | 0.448 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.448 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.448 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.448 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.448 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.448 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.448 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.447 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.447 | |
| 3bzu | A21 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3d75 | NBB | Pheromone-binding protein ASP1 | / | 0.447 | |
| 3v4e | COA | Putative acetyltransferase SACOL2570 | 2.3.1 | 0.447 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.446 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.446 | |
| 3pm0 | BHF | Cytochrome P450 1B1 | / | 0.446 | |
| 3tgu | WF3 | Cytochrome b | / | 0.446 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.446 | |
| 1fp1 | HCC | Isoliquiritigenin 2'-O-methyltransferase | / | 0.445 | |
| 1yin | CM3 | Estrogen receptor | / | 0.445 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.445 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.445 | |
| 3bfa | 9OD | Odorant binding protein ASP1 | / | 0.445 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.445 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.444 | |
| 1err | RAL | Estrogen receptor | / | 0.444 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 1ppj | ANY | Cytochrome b | / | 0.444 | |
| 2c7g | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.444 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.444 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.444 | |
| 3new | 3NE | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.444 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.444 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.444 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.444 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.443 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.443 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 3up0 | D7S | aceDAF-12 | / | 0.443 | |
| 3wix | LC3 | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.443 | |
| 4bfp | SWY | Tankyrase-2 | 2.4.2.30 | 0.443 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.443 | |
| 4jvl | EST | Estrogen sulfotransferase | 2.8.2.4 | 0.443 | |
| 4kwi | 1TJ | Reductase homolog | / | 0.443 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.443 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.443 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.443 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.442 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.442 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.442 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.442 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.441 | |
| 1xdk | REA | Retinoic acid receptor beta | / | 0.441 | |
| 1zhw | HC2 | Oxysterol-binding protein homolog 4 | / | 0.441 | |
| 2q66 | ATP | Poly(A) polymerase | 2.7.7.19 | 0.441 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.441 | |
| 2vxo | XMP | GMP synthase [glutamine-hydrolyzing] | 6.3.5.2 | 0.441 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 3zze | 6XP | Hepatocyte growth factor receptor | 2.7.10.1 | 0.441 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.441 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.441 | |
| 4nr4 | 2LK | CREB-binding protein | / | 0.441 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 4xiv | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.441 | |
| 4yt5 | H4M | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | / | 0.441 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.441 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.440 | |
| 1m7a | MQU | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2r3y | VAL_TYR_TRP_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.440 | |
| 2wpw | ACO | Orf14 | / | 0.440 | |
| 3dmj | GWE | Pol protein | / | 0.440 | |
| 3h1j | SMA | Cytochrome b | / | 0.440 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.440 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.440 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.440 | |
| 4i3v | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.440 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.440 |