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 |
|---|---|---|---|
| 2x2r | X2O | Kinesin-like protein KIF11 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2x2r | X2O | Kinesin-like protein KIF11 | / | 1.000 | |
| 3ken | ZZD | Kinesin-like protein KIF11 | / | 0.607 | |
| 2x7e | X7E | Kinesin-like protein KIF11 | / | 0.599 | |
| 2wog | ZZD | Kinesin-like protein KIF11 | / | 0.594 | |
| 2ieh | MOY | Kinesin-like protein KIF11 | / | 0.586 | |
| 2x7d | EGB | Kinesin-like protein KIF11 | / | 0.585 | |
| 4bbg | V02 | Kinesin-like protein KIF11 | / | 0.578 | |
| 2fme | 3QC | Kinesin-like protein KIF11 | / | 0.569 | |
| 2q2z | MKK | Kinesin-like protein KIF11 | / | 0.566 | |
| 1q0b | NAT | Kinesin-like protein KIF11 | / | 0.564 | |
| 1x88 | NAT | Kinesin-like protein KIF11 | / | 0.559 | |
| 4a51 | DQ8 | Kinesin-like protein KIF11 | / | 0.557 | |
| 2g1q | N9H | Kinesin-like protein KIF11 | / | 0.556 | |
| 2xae | 2XA | Kinesin-like protein KIF11 | / | 0.553 | |
| 3k3b | L31 | Kinesin-like protein KIF11 | / | 0.543 | |
| 2gm1 | 2AZ | Kinesin-like protein KIF11 | / | 0.531 | |
| 3k5e | K5E | Kinesin-like protein KIF11 | / | 0.523 | |
| 4as7 | 6LX | Kinesin-like protein KIF11 | / | 0.520 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.486 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.480 | |
| 2brm | DFZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.479 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.479 | |
| 4a5y | G7X | Kinesin-like protein KIF11 | / | 0.476 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.475 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.473 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.472 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.471 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.470 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.470 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.469 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.468 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.468 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.468 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.467 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.467 | |
| 2c3c | NAP | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.464 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.464 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.464 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.463 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.462 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 2qi3 | MZ5 | Gag-Pol polyprotein | / | 0.462 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4nt0 | 3DU | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.462 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 2gpv | OHT | Estrogen-related receptor gamma | / | 0.460 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.460 | |
| 3qx4 | X4B | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.460 | |
| 2wi1 | ZZ2 | Heat shock protein HSP 90-alpha | / | 0.459 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 1jhr | P2P | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.458 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.458 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.458 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.457 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3nuu | JOZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.457 | |
| 4ftr | 5HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.456 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.456 | |
| 2wmv | ZYV | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.456 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.455 | |
| 2c3l | IDZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.455 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.455 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.454 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.454 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.453 | |
| 2cch | ATP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 3nie | ANP | Mitogen-activated protein kinase | / | 0.453 | |
| 4d9t | 0JG | Ribosomal protein S6 kinase alpha-3 | 2.7.11.1 | 0.453 | |
| 1uu7 | BI2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.452 | |
| 2e9o | A58 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.452 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1lso | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 1tf7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.451 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.451 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4hyi | 1AO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 5cyo | GDP | Septin-9 | / | 0.451 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2vci | 2GJ | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 4ftt | 6HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 4oac | ADP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.450 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1phk | ATP | Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform | 2.7.11.19 | 0.449 | |
| 2hxl | 422 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 4yqf | GDP | Septin-9 | / | 0.449 | |
| 1u9i | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.448 | |
| 2uxu | NAR | HTH-type transcriptional regulator TtgR | / | 0.448 | |
| 3rni | 21Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.448 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.447 | |
| 3b89 | 5GP | 16S rRNA methylase | / | 0.447 | |
| 3h3c | P1E | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.447 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4rcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.447 | |
| 2brn | DF1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 2gpu | OHT | Estrogen-related receptor gamma | / | 0.446 | |
| 4ek6 | 10K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 4fsy | HK7 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1q3q | ANP | Thermosome subunit alpha | / | 0.445 | |
| 3qrt | X14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 4erw | STU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 4fsm | HK1 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 4jlt | 8PR | Cytochrome P450 2B4 | 1.14.14.1 | 0.445 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 1l4e | RBZ | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.444 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.444 | |
| 1os1 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.444 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1uvr | BI8 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.444 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.444 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.444 | |
| 3zew | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.444 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.444 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1ogu | ST8 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.443 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.443 | |
| 2yex | YEX | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 3ddq | RRC | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3upf | 0BU | Polyprotein | / | 0.443 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4ce3 | L4V | ATP-dependent molecular chaperone HSP82 | / | 0.443 | |
| 4ft3 | H1K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 4mcc | 21X | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.443 | |
| 4n49 | MGT | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 | 2.1.1.57 | 0.443 | |
| 2br1 | PFP | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2ceo | T44 | Thyroxine-binding globulin | / | 0.442 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.442 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 2uvz | GVJ | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2xj1 | XJ1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.442 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.442 | |
| 3uic | 09T | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 3x2e | NAI | Adenosylhomocysteinase | / | 0.442 | |
| 4fa6 | 0TA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4h0y | LAR | Actin, alpha skeletal muscle | / | 0.442 | |
| 5ack | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 1dj3 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.441 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.441 | |
| 2ijg | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.441 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.440 | |
| 2pmn | K51 | Protein kinase 7 | / | 0.440 | |
| 2q5k | AB1 | Protease | / | 0.440 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2wmt | ZYT | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2x1n | X1N | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 3flz | FLZ | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.440 | |
| 4fki | 09K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4gu6 | 10N | Focal adhesion kinase 1 | 2.7.10.2 | 0.440 | |
| 4hyh | 1AM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.440 | |
| 4rrv | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 5l7i | VIS | Smoothened homolog | / | 0.440 |