sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4uxx | ACP | Diacylglycerol kinase | 2.7.1.107 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4uxx | ACP | Diacylglycerol kinase | 2.7.1.107 | 1.000 | |
| 2o12 | FMN | Chorismate synthase | / | 0.508 | |
| 3lu6 | IMX | Serum albumin | / | 0.497 | |
| 1i44 | ACP | Insulin receptor | 2.7.10.1 | 0.489 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.485 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.484 | |
| 3cd5 | 7HI | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.477 | |
| 2zbz | VDX | Vitamin D3 dihydroxylase | / | 0.475 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.475 | |
| 4tv3 | ML9 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.475 | |
| 2qoq | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.474 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.474 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.473 | |
| 3a8t | ATP | Adenylate isopentenyltransferase | / | 0.473 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.473 | |
| 4xey | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.473 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.472 | |
| 2bx8 | AZQ | Serum albumin | / | 0.472 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.470 | |
| 2o2u | 738 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.470 | |
| 1uu8 | BI1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.468 | |
| 4k33 | ACP | Fibroblast growth factor receptor 3 | 2.7.10.1 | 0.468 | |
| 1cm8 | ANP | Mitogen-activated protein kinase 12 | / | 0.467 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.467 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.467 | |
| 1g69 | TZP | Thiamine-phosphate synthase | / | 0.466 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.466 | |
| 4jia | 1K3 | Tyrosine-protein kinase JAK2 | / | 0.466 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.465 | |
| 2hen | ADP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.465 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.465 | |
| 4uux | APR | CinA-like protein | / | 0.465 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.464 | |
| 3w0p | ADP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.464 | |
| 4hyu | 1BK | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.464 | |
| 1g67 | TZP | Thiamine-phosphate synthase | / | 0.463 | |
| 2buj | STU | Serine/threonine-protein kinase 16 | / | 0.463 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.463 | |
| 4mq1 | 2C3 | Dual specificity tyrosine-phosphorylation-regulated kinase 1A | 2.7.12.1 | 0.463 | |
| 3b9l | AZZ | Serum albumin | / | 0.462 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.461 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.460 | |
| 2oor | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.460 | |
| 2q6c | HR1 | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.460 | |
| 1g6c | IFP | Thiamine-phosphate synthase | / | 0.459 | |
| 1g4s | TPS | Thiamine-phosphate synthase | / | 0.458 | |
| 1nm1 | ATP | Major actin | / | 0.458 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.458 | |
| 2xrw | ANP | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.457 | |
| 4xx9 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.457 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.457 | |
| 2bun | FAD | AppA protein | / | 0.456 | |
| 2zdt | 46C | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.456 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.456 | |
| 4cta | ATP | CinA-like protein | / | 0.456 | |
| 4qx5 | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.456 | |
| 1g6c | TZP | Thiamine-phosphate synthase | / | 0.455 | |
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 | 0.455 | |
| 2c6e | HPM | Aurora kinase A | 2.7.11.1 | 0.454 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.454 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.454 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.453 | |
| 2bxn | IDB | Serum albumin | / | 0.453 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.453 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.453 | |
| 3lu8 | IQX | Serum albumin | / | 0.453 | |
| 3sc1 | 3S1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.453 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.453 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 4gvj | ADP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.453 | |
| 1dnp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.452 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.452 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 2b9f | ADP | Mitogen-activated protein kinase FUS3 | 2.7.11.24 | 0.452 | |
| 2biy | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.452 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.452 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.452 | |
| 4rkd | KET | Aminotransferase | / | 0.452 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.451 | |
| 3fro | NHF | GlgA glycogen synthase | / | 0.451 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.451 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4mcv | 29K | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.451 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.451 | |
| 1dq8 | COA | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.450 | |
| 3cy2 | MB9 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.450 | |
| 3dj4 | UD1 | Bifunctional protein GlmU | / | 0.450 | |
| 3tjs | D0R | Cytochrome P450 3A4 | / | 0.450 | |
| 4xf7 | ACP | Carbohydrate/pyrimidine kinase, PfkB family | / | 0.450 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.449 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.449 | |
| 2bxm | IMN | Serum albumin | / | 0.449 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 2yk2 | YJW | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 3fi3 | JK2 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.449 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.449 | |
| 3zw3 | ZW3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.449 | |
| 4z69 | DIF | Serum albumin | / | 0.449 | |
| 2b1p | AIZ | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.448 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.448 | |
| 3w0q | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.448 | |
| 4izy | 1J2 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.448 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.448 | |
| 1kor | ANP | Argininosuccinate synthase | / | 0.447 | |
| 1u5r | ATP | Serine/threonine-protein kinase TAO2 | 2.7.11.1 | 0.447 | |
| 2bhi | SFT | Cytotoxin 3 | / | 0.447 | |
| 2h8h | H8H | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.447 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.447 | |
| 3t8o | ATP | Rhodopsin kinase | / | 0.447 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.447 | |
| 3vf2 | ADP | nebramycin 5' synthase | 6.1.2.2 | 0.447 | |
| 4c4f | 7CE | Dual specificity protein kinase TTK | 2.7.12.1 | 0.447 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 4kqw | NAP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.447 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1hk2 | T44 | Serum albumin | / | 0.446 | |
| 1ihy | APR | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.446 | |
| 1ir3 | ANP | Insulin receptor | 2.7.10.1 | 0.446 | |
| 1j7k | ATP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.446 | |
| 1ol7 | ADP | Aurora kinase A | 2.7.11.1 | 0.446 | |
| 2izu | P01 | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.446 | |
| 2np8 | CC3 | Aurora kinase A | 2.7.11.1 | 0.446 | |
| 3pjc | PJC | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.446 | |
| 3pre | 3RE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4g3p | UD1 | Bifunctional protein GlmU | / | 0.446 | |
| 4jrn | ANP | Rhoptry kinase family protein | / | 0.446 | |
| 4qml | ANP | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.446 | |
| 1hk1 | T44 | Serum albumin | / | 0.445 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.445 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.445 | |
| 2dpx | GDP | GTP-binding protein RAD | / | 0.445 | |
| 2hxl | 422 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3l08 | ZIG | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 3vs3 | VSE | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.445 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.445 | |
| 4gk4 | L90 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.445 | |
| 4gmy | 0X5 | Tyrosine-protein kinase JAK2 | / | 0.445 | |
| 4ysw | FAD | Xanthine dehydrogenase/oxidase | / | 0.445 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.445 | |
| 1nmd | ATP | Major actin | / | 0.444 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.444 | |
| 2x5z | GDD | Mannose-1-phosphate guanylyltransferase | / | 0.444 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.444 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.444 | |
| 3igo | ANP | Calmodulin-domain protein kinase 1, putative | / | 0.444 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 4awi | AQ2 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.444 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.444 | |
| 4dca | ADP | Aminoglycoside phosphotransferase | / | 0.444 | |
| 4ejg | NCT | Cytochrome P450 2A13 | 1.14.14.1 | 0.444 | |
| 4fl2 | ANP | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.444 | |
| 5e92 | ANP | TGF-beta receptor type-2 | 2.7.11.30 | 0.444 | |
| 1pmv | 537 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.443 | |
| 1qmf | KEF | Penicillin-binding protein 2x | / | 0.443 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.443 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.443 | |
| 2exc | JNK | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.443 | |
| 2f5z | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.443 | |
| 3niz | ADP | Cdc2-like CDK2/CDC28 like protein kinase | / | 0.443 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.443 | |
| 3vgl | ANP | Glucokinase | / | 0.443 | |
| 3zv6 | 4HB | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.443 | |
| 4bi0 | Z0W | Dual specificity protein kinase TTK | 2.7.12.1 | 0.443 | |
| 1g41 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.442 | |
| 1i59 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 1m17 | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.442 | |
| 3fls | FLS | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3upf | 0BU | Polyprotein | / | 0.442 | |
| 4be7 | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.442 | |
| 4bi1 | ZO6 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.442 | |
| 4hmv | WUB | Phenazine biosynthesis protein PhzG | 1.4 | 0.442 | |
| 1g28 | FMN | PHY3 | / | 0.441 | |
| 1pag | FMP | Antiviral protein I | 3.2.2.22 | 0.441 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.441 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.441 | |
| 1xjj | DGT | Vitamin B12-dependent ribonucleotide reductase | / | 0.441 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2itu | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.441 | |
| 3eem | 53V | Uncharacterized protein | / | 0.441 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.441 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 3pnl | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.441 | |
| 3vqv | ANP | Pyrrolysine--tRNA ligase | / | 0.441 | |
| 4ie6 | UN9 | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.441 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4m69 | ANP | Receptor-interacting serine/threonine-protein kinase 3 | 2.7.11.1 | 0.441 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 1i58 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.440 | |
| 1ih8 | APC | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.440 | |
| 1m51 | TSX | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.440 | |
| 2fna | ADP | Uncharacterized protein | / | 0.440 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.440 | |
| 2ghm | LIC | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 2o0u | C0M | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.440 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 3d83 | GK6 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3el2 | ATP | Actin-5C | / | 0.440 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.440 | |
| 3w0r | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.440 | |
| 4k18 | 1OB | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.440 |