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 |
|---|---|---|---|
| 2bxe | 1FL | Serum albumin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2bxe | 1FL | Serum albumin | / | 1.000 | |
| 2bxg | IBP | Serum albumin | / | 0.540 | |
| 4zbr | NPS | Serum albumin | / | 0.527 | |
| 4ot2 | NPS | Serum albumin | / | 0.508 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.476 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.475 | |
| 3jwc | EKB | Dihydrofolate reductase | / | 0.475 | |
| 3zcw | 4A2 | Kinesin-like protein KIF11 | / | 0.473 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.469 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.469 | |
| 1sej | F89 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.467 | |
| 1u28 | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.464 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.464 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.463 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.463 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.462 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 4bbg | V02 | Kinesin-like protein KIF11 | / | 0.462 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.461 | |
| 3tdl | 11D | Serum albumin | / | 0.460 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.459 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.459 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.459 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.459 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.457 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.457 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.457 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.457 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.457 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.457 | |
| 4h4u | NDP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.457 | |
| 1yw2 | PGJ | Mitogen-activated protein kinase 14 | / | 0.456 | |
| 2w3v | TOP | Dihydrofolate reductase | / | 0.456 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 3srq | Q19 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.456 | |
| 4b99 | R4L | Mitogen-activated protein kinase 7 | 2.7.11.24 | 0.456 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.456 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 2hfp | NSI | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.455 | |
| 4joa | 3DK | ALK tyrosine kinase receptor | 2.7.10.1 | 0.455 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.454 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.454 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.454 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.454 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 2ze2 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.453 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.453 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.453 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 1bve | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.451 | |
| 1pg3 | PRX | Acetyl-coenzyme A synthetase | / | 0.451 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 1zhz | ERG | Oxysterol-binding protein homolog 4 | / | 0.451 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.451 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.451 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.451 | |
| 4l3j | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.451 | |
| 2izr | BRK | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.450 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.450 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.450 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.449 | |
| 2gn9 | UPG | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.449 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.449 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.449 | |
| 4aw3 | MYV | Mycinamicin IV hydroxylase/epoxidase | / | 0.449 | |
| 4bc6 | XZN | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.449 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.448 | |
| 2dq7 | STU | Tyrosine-protein kinase Fyn | 2.7.10.2 | 0.448 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.448 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.448 | |
| 1qvn | FRI | Interleukin-2 | / | 0.447 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.447 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.447 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.447 | |
| 3au8 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.447 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.447 | |
| 3zsi | 52P | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 4inb | 1F6 | Gag protein | / | 0.447 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.447 | |
| 4k11 | 0J9 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.447 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.447 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.447 | |
| 1hwz | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.446 | |
| 1i3m | UD1 | UDP-glucose 4-epimerase | / | 0.446 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.446 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.446 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2rf2 | MRX | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.446 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.445 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.445 | |
| 4l9q | 9TP | Serum albumin | / | 0.445 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.445 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2c47 | 5ID | Casein kinase I isoform gamma-2 | / | 0.444 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.444 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3frd | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.444 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.444 | |
| 3w2o | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.444 | |
| 4h4q | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.444 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.444 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.444 | |
| 5eyp | LOC | Tubulin beta chain | / | 0.444 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.443 | |
| 3nwy | GTP | Uridylate kinase | / | 0.443 | |
| 3qw4 | U5P | Orotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative | / | 0.443 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.443 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.443 | |
| 4feq | 0T8 | Tyrosine-protein kinase receptor TYRO3 | 2.7.10.1 | 0.443 | |
| 4fgg | 0U5 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 5dt4 | ATP | Aurora kinase A | 2.7.11.1 | 0.443 | |
| 5eox | ADP | Type 4 fimbrial biogenesis protein PilM | / | 0.443 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1qcj | APT | Antiviral protein I | 3.2.2.22 | 0.442 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.442 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2izt | 23D | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.442 | |
| 2p2m | PRX | Acetyl-coenzyme A synthetase | / | 0.442 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.442 | |
| 3lu8 | IQX | Serum albumin | / | 0.442 | |
| 3mec | 65B | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.442 | |
| 4nr4 | 2LK | CREB-binding protein | / | 0.442 | |
| 5doz | NDP | JamJ | / | 0.442 | |
| 1rbq | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.441 | |
| 1xl2 | 189 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1zhw | HC2 | Oxysterol-binding protein homolog 4 | / | 0.441 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3h0s | B38 | Acetyl-CoA carboxylase | / | 0.441 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.441 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.440 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 1tl1 | H18 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.440 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.440 | |
| 3f46 | I2C | 5,10-methenyltetrahydromethanopterin hydrogenase | 1.12.98.2 | 0.440 | |
| 3uzp | 0CK | Casein kinase I isoform delta | 2.7.11.1 | 0.440 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.440 | |
| 4c4j | X21 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.440 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.440 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.440 |