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 |
|---|---|---|---|
| 4fok | C2E | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4fok | C2E | Uncharacterized protein | / | 1.000 | |
| 4foj | C2E | Uncharacterized protein | / | 0.706 | |
| 4f48 | C2E | Uncharacterized protein | / | 0.539 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.496 | |
| 2ceo | T44 | Thyroxine-binding globulin | / | 0.492 | |
| 2j7t | 274 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.489 | |
| 4y12 | AGS | Serine/threonine-protein kinase PknG | 2.7.11.1 | 0.484 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.482 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.482 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.481 | |
| 2jjk | R15 | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.478 | |
| 2q6c | HR1 | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.477 | |
| 3t9a | ANP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.476 | |
| 3tdl | 11D | Serum albumin | / | 0.476 | |
| 4hjf | C2E | GGDEF family protein | / | 0.476 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.476 | |
| 3ake | C5P | Cytidylate kinase | / | 0.475 | |
| 4at8 | ATP | Interleukin enhancer-binding factor 2 | / | 0.475 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.474 | |
| 4c1f | X8Z | Metallo-beta-lactamase type 2 | / | 0.474 | |
| 1q97 | ATP | Serine/threonine-protein kinase SKY1 | 2.7.11.1 | 0.473 | |
| 3tm0 | ANP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.473 | |
| 5ify | TRH | Glucose-1-phosphate thymidylyltransferase | / | 0.472 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.471 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.470 | |
| 3qc9 | ADP | Rhodopsin kinase | / | 0.470 | |
| 2ghm | LIC | Mitogen-activated protein kinase 14 | / | 0.468 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.467 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.466 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.466 | |
| 4f9w | LM4 | Mitogen-activated protein kinase 14 | / | 0.466 | |
| 3zxt | ACP | Death-associated protein kinase 1 | 2.7.11.1 | 0.465 | |
| 4tv3 | ML9 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.465 | |
| 5ce3 | ADP | Protein kinase YopO | / | 0.465 | |
| 4ix5 | ANP | Uncharacterized protein | / | 0.464 | |
| 5c03 | AGS | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.464 | |
| 2bxe | 1FL | Serum albumin | / | 0.463 | |
| 4xx9 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.463 | |
| 1ee0 | CAA | 2-pyrone synthase | / | 0.462 | |
| 2gn9 | UPG | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.462 | |
| 3x2v | ATP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.462 | |
| 2q66 | ATP | Poly(A) polymerase | 2.7.7.19 | 0.461 | |
| 3c4w | ATP | Rhodopsin kinase | / | 0.461 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.460 | |
| 3nsz | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.460 | |
| 3wow | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.460 | |
| 4ekk | ANP | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.460 | |
| 1zq9 | SAM | Probable dimethyladenosine transferase | / | 0.459 | |
| 2x60 | GTP | Mannose-1-phosphate guanylyltransferase | / | 0.459 | |
| 1g4s | TPS | Thiamine-phosphate synthase | / | 0.458 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.458 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.458 | |
| 3spt | UD1 | Bifunctional protein GlmU | / | 0.458 | |
| 1v9n | NDP | Malate dehydrogenase | 1.1.1.37 | 0.457 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.457 | |
| 3kbz | 2T4 | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.457 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.457 | |
| 4awg | CI3 | Polymerase acidic protein | / | 0.457 | |
| 4en4 | ATP | Pyridoxal kinase | 2.7.1.35 | 0.457 | |
| 4i3z | ADP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.457 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.456 | |
| 2cjm | ATP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.456 | |
| 3kc0 | 2T5 | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.456 | |
| 3kmw | ATP | Integrin-linked protein kinase | 2.7.11.1 | 0.456 | |
| 3w0p | ADP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.456 | |
| 4fl1 | ANP | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.456 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.456 | |
| 3ef5 | DGT | Probable pyrophosphohydrolase | / | 0.455 | |
| 3sjz | GNP | Translation initiation factor 2 subunit gamma | / | 0.455 | |
| 4wq5 | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.455 | |
| 1hk3 | T44 | Serum albumin | / | 0.454 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.454 | |
| 3lmg | ANP | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.454 | |
| 3ub5 | ATP | Actin, cytoplasmic 1 | / | 0.454 | |
| 4c3p | ACP | Aurora kinase A | 2.7.11.1 | 0.454 | |
| 4ot2 | NPS | Serum albumin | / | 0.454 | |
| 1lrl | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.453 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.453 | |
| 2zbz | VDX | Vitamin D3 dihydroxylase | / | 0.453 | |
| 4c4h | 7RO | Dual specificity protein kinase TTK | 2.7.12.1 | 0.453 | |
| 4f07 | FAD | Styrene monooxygenase component 2 | / | 0.453 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.453 | |
| 4zbr | NPS | Serum albumin | / | 0.453 | |
| 3juk | UPG | UTP--glucose-1-phosphate uridylyltransferase | / | 0.452 | |
| 3sjh | LAR | Actin, alpha skeletal muscle | / | 0.452 | |
| 4bew | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.452 | |
| 4nxw | ADP | Mitochondrial dynamics protein MID51 | / | 0.452 | |
| 4zrn | UPG | UDP-glucose 4-epimerase, putative | / | 0.452 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.452 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.451 | |
| 2gej | GDD | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.451 | |
| 2qr1 | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.451 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.451 | |
| 4pl3 | ADP | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.451 | |
| 4xjx | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.451 | |
| 4zas | TYD | CalS13 | / | 0.451 | |
| 1aj8 | COA | Citrate synthase | / | 0.450 | |
| 1xr1 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.450 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 3lu7 | IPX | Serum albumin | / | 0.450 | |
| 4awk | CI1 | Polymerase acidic protein | / | 0.450 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 5f1c | ATP | Uncharacterized protein | / | 0.450 | |
| 1ict | T44 | Transthyretin | / | 0.449 | |
| 1w87 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.449 | |
| 2buj | STU | Serine/threonine-protein kinase 16 | / | 0.449 | |
| 2nom | DUT | Poly(A) polymerase, putative | / | 0.449 | |
| 3l7l | C2G | Teichoic acid poly(glycerol phosphate) polymerase | / | 0.449 | |
| 4be7 | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.449 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.449 | |
| 4ii5 | ADP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 4nzo | ANP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.449 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.449 | |
| 4oa9 | ANP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.449 | |
| 4riy | ANP | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.449 | |
| 5dos | ATP | Aurora kinase A | 2.7.11.1 | 0.449 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.449 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.449 | |
| 1tz8 | DES | Transthyretin | / | 0.448 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.448 | |
| 3dqw | AGS | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.448 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.448 | |
| 4fic | 0UL | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.448 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.448 | |
| 1uu3 | LY4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.447 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.447 | |
| 3eku | ATP | Actin-5C | / | 0.447 | |
| 4fl3 | ANP | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.447 | |
| 4gyi | ADP | Uncharacterized protein | / | 0.447 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.447 | |
| 4n9w | GDP | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.447 | |
| 1o6y | ACP | Serine/threonine-protein kinase PknB | 2.7.11.1 | 0.446 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.446 | |
| 2ati | IHU | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.446 | |
| 2bx8 | AZQ | Serum albumin | / | 0.446 | |
| 3cd5 | 7HI | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.446 | |
| 3uvp | 048 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 4o6m | C5P | Uncharacterized protein | / | 0.446 | |
| 4wbb | ADP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 1ie4 | T44 | Transthyretin | / | 0.445 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.445 | |
| 1q3g | UDA | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.445 | |
| 2cmk | CDP | Cytidylate kinase | 2.7.4.25 | 0.445 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.445 | |
| 3fpb | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.445 | |
| 4a0m | NAD | Betaine aldehyde dehydrogenase, chloroplastic | 1.2.1.8 | 0.445 | |
| 4dee | ADP | Aurora kinase A | 2.7.11.1 | 0.445 | |
| 4o0u | ADN | Aurora kinase A | 2.7.11.1 | 0.445 | |
| 4rqv | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 4xey | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.445 | |
| 1hk1 | T44 | Serum albumin | / | 0.444 | |
| 1i44 | ACP | Insulin receptor | 2.7.10.1 | 0.444 | |
| 2g9u | G27 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.444 | |
| 3dj4 | UD1 | Bifunctional protein GlmU | / | 0.444 | |
| 3pju | C2E | Diguanylate cyclase/phosphodiesterase | / | 0.444 | |
| 3zcw | 4A2 | Kinesin-like protein KIF11 | / | 0.444 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.444 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.444 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 4l9i | 8PR | Rhodopsin kinase | / | 0.444 | |
| 4mxo | DB8 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.444 | |
| 1os1 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.443 | |
| 2ydf | IO3 | Serum albumin | / | 0.443 | |
| 3dga | RJ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3uhm | RFN | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.443 | |
| 3vth | APC | Carbamoyltransferase | / | 0.443 | |
| 1adc | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1lco | PPY | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.442 | |
| 1mab | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.442 | |
| 1uu8 | BI1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.442 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2mjp | ANP | dITP/XTP pyrophosphatase | 3.6.1.19 | 0.442 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.442 | |
| 2pyw | ADP | Methylthioribose kinase | 2.7.1.100 | 0.442 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.442 | |
| 3mfu | ANP | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.442 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.442 | |
| 4eym | 0RX | Mitogen-activated protein kinase 13 | 2.7.11.24 | 0.442 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.442 | |
| 2bu2 | ATP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.441 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.441 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.441 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 4beb | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.441 | |
| 4eht | ADP | 2-hydroxyisocaproyl-CoA dehydratase activator | / | 0.441 | |
| 4i3p | 1CW | 3-hydroxyanthranilate 3,4-dioxygenase | / | 0.441 | |
| 4rqk | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4ydu | ADP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.441 | |
| 5kf1 | ACO | Predicted acetyltransferase | / | 0.441 | |
| 1h6v | NDP | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.440 | |
| 1kk4 | ACO | Streptogramin A acetyltransferase | 2.3.1 | 0.440 | |
| 1t9b | 1CS | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.440 | |
| 1wc1 | TAT | Adenylate cyclase | / | 0.440 | |
| 2b9f | ADP | Mitogen-activated protein kinase FUS3 | 2.7.11.24 | 0.440 | |
| 2bu8 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.440 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3l08 | ZIG | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4f7l | 0SO | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.440 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 4m69 | ANP | Receptor-interacting serine/threonine-protein kinase 3 | 2.7.11.1 | 0.440 | |
| 4oag | ADP | Mitochondrial dynamics protein MID51 | / | 0.440 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.440 | |
| 4ysj | ADP | Calmodulin-like domain protein kinase | / | 0.440 | |
| 4z69 | DIF | Serum albumin | / | 0.440 |