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 |
|---|---|---|---|
| 3bv2 | P38 | Mitogen-activated protein kinase 14 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 1.000 | |
| 3bv3 | P39 | Mitogen-activated protein kinase 14 | / | 0.497 | |
| 3e92 | G6A | Mitogen-activated protein kinase 14 | / | 0.492 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.486 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.486 | |
| 3bx5 | 304 | Mitogen-activated protein kinase 14 | / | 0.477 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.472 | |
| 4eh6 | 0ON | Mitogen-activated protein kinase 14 | / | 0.471 | |
| 1osv | CHC | Bile acid receptor | / | 0.468 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.466 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 3mpt | 1GK | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.465 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 3lfa | 1N1 | Mitogen-activated protein kinase 14 | / | 0.464 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.462 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.461 | |
| 3iph | G11 | Mitogen-activated protein kinase 14 | / | 0.461 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.461 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.460 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.459 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.459 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.458 | |
| 1t7k | BH0 | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.458 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 2bal | PQA | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.457 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.457 | |
| 3l8x | N4D | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.456 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1siv | PSI | Gag-Pol polyprotein | / | 0.456 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.456 | |
| 2i4u | DJR | Protease | / | 0.456 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.456 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.456 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.456 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.455 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.455 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.455 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.455 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.455 | |
| 1bv9 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.454 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.454 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.453 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.453 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 3i7e | DJR | Gag-Pol polyprotein | / | 0.453 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.453 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.452 | |
| 2rg6 | 287 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 3tog | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.452 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 5cyo | GDP | Septin-9 | / | 0.452 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4zs2 | FLU | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.451 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.450 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.450 | |
| 2avv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 2qen | ADP | Walker-Type ATPase | / | 0.450 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.450 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.450 | |
| 3r2b | 05B | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.450 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.450 | |
| 4i4b | 1CV | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.450 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 1hsg | MK1 | Gag-Pol polyprotein | / | 0.449 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.449 | |
| 2pwr | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.448 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 2zb0 | GK3 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4a4q | UX9 | Pol protein | / | 0.448 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.447 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.447 | |
| 3aid | ARQ | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.447 | |
| 4h4u | NDP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.447 | |
| 4jaz | STL | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 4kb9 | G79 | Protease | / | 0.447 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.447 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.447 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.446 | |
| 2rg5 | 279 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.446 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.446 | |
| 3kp4 | MII | Transcriptional regulator TcaR | / | 0.446 | |
| 3pj8 | 404 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.446 | |
| 5a3c | NAD | SIR2 family protein | / | 0.446 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1ezv | UQ6 | Cytochrome b | / | 0.445 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.445 | |
| 2gtm | LID | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3ec0 | GRL | Gag-Pol polyprotein | 3.4.23.47 | 0.445 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3kfr | 3TL | Gag-Pol polyprotein | / | 0.445 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.444 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.444 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.444 | |
| 2pwc | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.444 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.444 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.444 | |
| 3mxd | K53 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3o9h | K2E | Gag-Pol polyprotein | / | 0.444 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.444 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.443 | |
| 1sgu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2i0a | MUI | Protease | / | 0.443 | |
| 2psu | MUU | Protease | / | 0.443 | |
| 2qnn | QN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2rkf | AB1 | Pol protein | / | 0.443 | |
| 3h59 | H59 | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.443 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.443 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.443 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.442 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.442 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.442 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.442 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1z1r | HBH | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 2zaz | GK1 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.441 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.441 | |
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.441 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.441 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.440 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.440 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.440 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.440 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.440 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.440 | |
| 3tqa | NDP | Dihydrofolate reductase | / | 0.440 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4fdn | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.440 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.440 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4qec | NAP | ElxO | / | 0.440 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.440 |