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 |
|---|---|---|---|
| 2ce7 | ADP | ATP-dependent zinc metalloprotease FtsH |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ce7 | ADP | ATP-dependent zinc metalloprotease FtsH | / | 1.000 | |
| 2cea | ADP | ATP-dependent zinc metalloprotease FtsH | / | 0.577 | |
| 4ww0 | ADP | ATP-dependent zinc metalloprotease FtsH | / | 0.521 | |
| 1e32 | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.514 | |
| 1s3s | ADP | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.500 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.488 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.487 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.476 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.476 | |
| 1vjy | 460 | TGF-beta receptor type-1 | 2.7.11.30 | 0.474 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.472 | |
| 1ofh | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.471 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.469 | |
| 2gr0 | ADP | Ferredoxin reductase | / | 0.469 | |
| 4bdc | ODH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.469 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.469 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.467 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.467 | |
| 4d81 | ADP | AAA ATPase, central domain protein | / | 0.466 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.463 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.462 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.462 | |
| 3hrc | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.461 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.461 | |
| 1dq9 | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.460 | |
| 1l4m | NCN | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.460 | |
| 3rak | 03Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.460 | |
| 1ckp | PVB | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.459 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.458 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.458 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.458 | |
| 2w06 | FRV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.458 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.458 | |
| 1ovm | TPP | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.457 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.457 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.456 | |
| 4ros | APR | Malate dehydrogenase | / | 0.456 | |
| 1nht | PGS | Adenylosuccinate synthetase | / | 0.455 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.455 | |
| 4l42 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.454 | |
| 1cg1 | IMO | Adenylosuccinate synthetase | / | 0.453 | |
| 1h74 | AGS | Homoserine kinase | 2.7.1.39 | 0.453 | |
| 1iy8 | NAD | Levodione reductase | / | 0.453 | |
| 2vtn | LZ7 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 3hrf | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.453 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2nmx | M25 | Carbonic anhydrase 1 | 4.2.1.1 | 0.452 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.452 | |
| 3qcs | 3Q1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.452 | |
| 3vfq | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.452 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.452 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.452 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.452 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.451 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.451 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.451 | |
| 4izy | 1J2 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.451 | |
| 1qpb | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.450 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.450 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1y8y | CT7 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.449 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.449 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.449 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.449 | |
| 2d4v | NAD | Isocitrate dehydrogenase [NADP] | / | 0.448 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.448 | |
| 3qd3 | 3Q5 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 3zew | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.448 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1l4e | RBZ | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.447 | |
| 1lny | IMO | Adenylosuccinate synthetase isozyme 1 | / | 0.447 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.447 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.447 | |
| 2pzi | AXX | Serine/threonine-protein kinase PknG | 2.7.11.1 | 0.447 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.447 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 3rni | 21Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.447 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.447 | |
| 4jbq | VX6 | Aurora kinase A | 2.7.11.1 | 0.447 | |
| 1im2 | ADP | ATP-dependent protease ATPase subunit HslU | / | 0.446 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.446 | |
| 1ruo | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.446 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.446 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 2vk4 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.446 | |
| 2ydi | YDI | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.446 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.446 | |
| 3vey | 0H5 | Glucokinase | 2.7.1.2 | 0.446 | |
| 4a9u | A9U | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.446 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.445 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 2vto | LZ8 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 3lxp | IZA | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.445 | |
| 3r7u | X96 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 3she | I85 | MAP kinase-activated protein kinase 3 | 2.7.11.1 | 0.445 | |
| 4i7f | NVE | Gag-Pol polyprotein | 2.7.7.49 | 0.445 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.445 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.444 | |
| 1gii | 1PU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 1me8 | RVP | Inosine-5'-monophosphate dehydrogenase | / | 0.444 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.444 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.444 | |
| 4aa4 | QC0 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.444 | |
| 4fkj | 11K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.444 | |
| 1hk4 | T44 | Serum albumin | / | 0.443 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2ghm | LIC | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.443 | |
| 3zsi | 52P | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 4c3s | NAD | Aldehyde Dehydrogenase | / | 0.443 | |
| 4dlj | 6RG | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 4fks | 46K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 4jrn | ANP | Rhoptry kinase family protein | / | 0.443 | |
| 4lj5 | ADP | Chaperone protein ClpB | / | 0.443 | |
| 4lj8 | ADP | Chaperone protein ClpB | / | 0.443 | |
| 4pkg | ATP | Actin, alpha skeletal muscle | / | 0.443 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.443 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.442 | |
| 2bdf | 24A | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.442 | |
| 2cgx | 3D3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.442 | |
| 2q5p | 241 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3kt8 | LTN | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.442 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.442 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 4ct1 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 5c3c | ADP | CbbQ/NirQ/NorQ domain protein | / | 0.442 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.441 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.441 | |
| 2e2q | ADP | ATP-dependent hexokinase | / | 0.441 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.441 | |
| 2phk | ATP | Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform | 2.7.11.19 | 0.441 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 2rew | REW | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 3nun | JMZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.441 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.441 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.441 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.441 | |
| 4jk3 | NAD | Uncharacterized protein | / | 0.441 | |
| 4o2b | LOC | Tubulin beta-2B chain | / | 0.441 | |
| 1e94 | ANP | ATP-dependent protease ATPase subunit HslU | / | 0.440 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.440 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2vth | LZ2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3thr | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.440 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.440 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.440 | |
| 4el5 | D1M | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.440 | |
| 4eon | 1RO | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4fki | 09K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4im0 | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.440 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.440 | |
| 4xey | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.440 | |
| 4z07 | PCG | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.440 |