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 |
|---|---|---|---|
| 3eva | SAH | Genome polyprotein | 2.1.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3eva | SAH | Genome polyprotein | 2.1.1.56 | 1.000 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.648 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.583 | |
| 2px2 | SAH | Genome polyprotein | 2.7.7.48 | 0.538 | |
| 3evc | SAH | Genome polyprotein | 2.1.1.56 | 0.534 | |
| 5cuq | NSC | Genome polyprotein | / | 0.529 | |
| 2p3q | SAH | Genome polyprotein | / | 0.526 | |
| 1l9k | SAH | Genome polyprotein | 2.7.7.48 | 0.520 | |
| 1r6a | SAH | Genome polyprotein | 2.7.7.48 | 0.510 | |
| 3p97 | SAM | Genome polyprotein | 2.1.1.56 | 0.501 | |
| 2p1d | SAH | Genome polyprotein | 2.7.7.48 | 0.500 | |
| 2px5 | SAH | Genome polyprotein | 2.7.7.48 | 0.493 | |
| 3ely | SAH | Methyltransferase | / | 0.493 | |
| 5jjr | SAH | Genome polyprotein | / | 0.492 | |
| 2oxt | SAM | Genome polyprotein | / | 0.490 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.489 | |
| 5dto | SAH | Genome polyprotein | / | 0.486 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.481 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.479 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.478 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.476 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.475 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.474 | |
| 1v79 | FR7 | Adenosine deaminase | 3.5.4.4 | 0.471 | |
| 3elu | SAM | Methyltransferase | / | 0.471 | |
| 5jjs | SAH | Genome polyprotein | / | 0.470 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.468 | |
| 4aw1 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.468 | |
| 2bxm | IMN | Serum albumin | / | 0.467 | |
| 4ctj | SAM | Genome polyprotein | / | 0.467 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.466 | |
| 3upf | 0BU | Polyprotein | / | 0.465 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.464 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.463 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.462 | |
| 3eld | SFG | Methyltransferase | / | 0.462 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.462 | |
| 3kdi | A8S | Abscisic acid receptor PYL2 | / | 0.462 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.462 | |
| 4n57 | ADP | APH(2'')-Id | / | 0.462 | |
| 2bkz | SBC | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.460 | |
| 4bb4 | 32W | Ephrin type-B receptor 4 | 2.7.10.1 | 0.460 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.460 | |
| 1jm6 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.459 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.459 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.459 | |
| 3hko | ANP | Calcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands | / | 0.458 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.457 | |
| 3zew | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.457 | |
| 4zs2 | FLU | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.457 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.456 | |
| 2vx1 | 7X8 | Ephrin type-B receptor 4 | 2.7.10.1 | 0.456 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.456 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 4eqc | XR1 | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.456 | |
| 4hjf | C2E | GGDEF family protein | / | 0.456 | |
| 1uu8 | BI1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.455 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.455 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.455 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.455 | |
| 1u59 | STU | Tyrosine-protein kinase ZAP-70 | 2.7.10.2 | 0.454 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.454 | |
| 3g2h | KOT | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.454 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.454 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.454 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.454 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.453 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.453 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.453 | |
| 4rqk | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.453 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.452 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.452 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.452 | |
| 3pxk | PXK | Focal adhesion kinase 1 | 2.7.10.2 | 0.452 | |
| 3u9n | 09H | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.452 | |
| 4yuq | KS1 | Calmodulin-like domain protein kinase | / | 0.452 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.451 | |
| 1r2j | FAD | FkbI | / | 0.451 | |
| 2brg | DFY | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 3cqu | CQU | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.451 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.451 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.451 | |
| 4hj3 | FMN | LOV protein | / | 0.451 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 1qpd | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.450 | |
| 1zar | ADP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.450 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.450 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1e9h | INR | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.449 | |
| 1ne6 | SP1 | cAMP-dependent protein kinase type I-alpha regulatory subunit | / | 0.449 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.449 | |
| 2izu | P01 | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.449 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.449 | |
| 2xyu | Q9G | Ephrin type-A receptor 4 | 2.7.10.1 | 0.449 | |
| 3b9l | AZZ | Serum albumin | / | 0.449 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 3l8x | N4D | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.449 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.449 | |
| 3qj7 | UMP | Thymidylate synthase ThyA | / | 0.449 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.449 | |
| 4d9f | DCS | D-cysteine desulfhydrase | / | 0.449 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.449 | |
| 5hyr | EST | Estrogen receptor | / | 0.449 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.448 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.448 | |
| 1lhw | ESM | Sex hormone-binding globulin | / | 0.448 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.448 | |
| 2bgj | FAD | NADPH:ferredoxin reductase | / | 0.448 | |
| 2bro | DF2 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2itw | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.448 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.448 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 3hrf | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 4fv8 | E63 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.448 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 4ogr | ADN | Cyclin-dependent kinase 9 | 2.7.11.22 | 0.448 | |
| 4ubt | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.448 | |
| 4xj4 | 3AT | Cyclic GMP-AMP synthase | / | 0.448 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.447 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.447 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.447 | |
| 1lhu | EST | Sex hormone-binding globulin | / | 0.447 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.447 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.447 | |
| 2y5s | 78H | Dihydropteroate synthase | / | 0.447 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3u9e | COA | Lmo1369 protein | / | 0.447 | |
| 4dh7 | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.446 | |
| 2gr0 | FAD | Ferredoxin reductase | / | 0.446 | |
| 3bhr | THG | Thymidylate synthase | / | 0.446 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.446 | |
| 1v7a | FRC | Adenosine deaminase | 3.5.4.4 | 0.445 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.445 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.445 | |
| 2wxv | WXV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 2xbj | XBJ | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.445 | |
| 3pjc | PJC | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.445 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4qmx | H8H | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.445 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.445 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.444 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.444 | |
| 1rl3 | PCG | cAMP-dependent protein kinase type I-alpha regulatory subunit | / | 0.444 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.444 | |
| 2wip | P49 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3zbx | 6XE | Hepatocyte growth factor receptor | 2.7.10.1 | 0.444 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.444 | |
| 4jq7 | KJQ | Epidermal growth factor receptor | 2.7.10.1 | 0.444 | |
| 4qna | X11 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.444 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.444 | |
| 1agw | SU2 | Fibroblast growth factor receptor 1 | / | 0.443 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.443 | |
| 2pwl | ACP | Fibroblast growth factor receptor 2 | / | 0.443 | |
| 2q46 | NAP | Uncharacterized protein At5g02240 | / | 0.443 | |
| 4ft3 | H1K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 4fyn | 0VE | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.443 | |
| 4u07 | ATP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.443 | |
| 4uoc | NCN | CinA-like protein | / | 0.443 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.443 | |
| 1j7k | ATP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.442 | |
| 1oky | STU | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 1x7e | 244 | Estrogen receptor | / | 0.442 | |
| 2adm | SAM | Modification methylase TaqI | 2.1.1.72 | 0.442 | |
| 2qhn | 582 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.442 | |
| 3ag9 | A02 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 3pd2 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.442 | |
| 4d9e | LCS | D-cysteine desulfhydrase | / | 0.442 | |
| 4j97 | ACP | Fibroblast growth factor receptor 2 | / | 0.442 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.442 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.442 | |
| 4qo9 | 627 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.442 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.442 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.442 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.441 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1yin | CM3 | Estrogen receptor | / | 0.441 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.441 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.441 | |
| 3op5 | REB | Serine/threonine-protein kinase VRK1 | 2.7.11.1 | 0.441 | |
| 3we4 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.441 | |
| 4hj4 | FMN | LOV protein | / | 0.441 | |
| 4qmy | STU | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.441 | |
| 1mew | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.440 | |
| 2e9u | A25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2ea1 | GPG | Ribonuclease I | 3.1.27.6 | 0.440 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.440 | |
| 2vd5 | BI8 | Myotonin-protein kinase | 2.7.11.1 | 0.440 | |
| 2wmr | ZYR | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.440 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.440 | |
| 3rwp | ABQ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3v8w | 0G2 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.440 | |
| 3vbq | 0F5 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.440 | |
| 4fl1 | ANP | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.440 | |
| 4gfg | 0XF | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.440 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4l7s | G7K | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.440 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.440 |