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 |
|---|---|---|---|
| 3zv5 | BPY | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3zv5 | BPY | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 1.000 | |
| 3zv6 | 4HB | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.631 | |
| 3dv3 | MEK | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.478 | |
| 4iwv | 1J9 | Glucokinase | 2.7.1.2 | 0.477 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.473 | |
| 5djt | FMN | NPH1-2 | / | 0.472 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.471 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.469 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3dds | 26B | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.467 | |
| 1j3k | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.466 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.464 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.464 | |
| 1g28 | FMN | PHY3 | / | 0.463 | |
| 2v1a | FMN | NPH1-1 | / | 0.463 | |
| 3up3 | XCA | aceDAF-12 | / | 0.463 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.463 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.461 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.460 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3cyz | 9OD | Pheromone-binding protein ASP1 | / | 0.460 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.460 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.460 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.459 | |
| 3v1s | 0LH | Strictosidine synthase | 4.3.3.2 | 0.459 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.459 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.458 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.457 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.457 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.457 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.457 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.457 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.457 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.456 | |
| 5dju | FMN | NPH1-2 | / | 0.455 | |
| 5hi6 | MTX | Dihydrofolate reductase | / | 0.455 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.454 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.454 | |
| 4a4w | YFB | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.453 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.453 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.453 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.453 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.452 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.452 | |
| 4bkj | STI | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.452 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.451 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.451 | |
| 2qk8 | MTX | Dihydrofolate reductase | / | 0.451 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.451 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.451 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.451 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.450 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1nbm | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.449 | |
| 3b9l | AZZ | Serum albumin | / | 0.449 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.449 | |
| 3zsg | T75 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.448 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.448 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.448 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.448 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.447 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.447 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.447 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.447 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.447 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.446 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.446 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.446 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.446 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4guk | P2G | Neuronal calcium sensor 1 | / | 0.445 | |
| 2jfz | 003 | Glutamate racemase | / | 0.444 | |
| 2xjj | L81 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.444 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.444 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.444 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.443 | |
| 3ans | S38 | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.443 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4f4q | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.443 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1h8h | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.442 | |
| 1h8h | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.442 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.442 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.442 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.441 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.441 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.441 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.441 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4xvr | GNP | GTPase HRas | / | 0.441 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.440 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.440 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.440 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 2xsz | ATP | RuvB-like 2 | 3.6.4.12 | 0.440 | |
| 3g8e | IS1 | Nicotinamide phosphoribosyltransferase | 2.4.2.12 | 0.440 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.440 | |
| 3p9t | TCL | Repressor | / | 0.440 |