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 |
|---|---|---|---|
| 4kgn | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4kgn | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 1.000 | |
| 4jal | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.565 | |
| 4pzk | SAH | Putative tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.556 | |
| 3nk7 | SAM | 23S rRNA (adenosine(1067)-2'-O)-methyltransferase | / | 0.515 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.513 | |
| 1mxi | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.505 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.490 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.489 | |
| 4cng | SAH | SpoU rRNA methylase | / | 0.485 | |
| 4yvk | SFG | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.484 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.482 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.482 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.482 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.480 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.479 | |
| 3pvc | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.479 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.478 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.478 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.478 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.475 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.475 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.473 | |
| 4xbo | SAH | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | 2.1.1.200 | 0.472 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.468 | |
| 2e8h | SAH | Diphthine synthase | / | 0.468 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.465 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.465 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.464 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.464 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.464 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.462 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.462 | |
| 1lrk | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.461 | |
| 2c3k | ABO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.461 | |
| 2dxv | SAH | Diphthine synthase | / | 0.461 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.461 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.461 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.461 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.461 | |
| 4dja | FAD | (6-4) photolyase | / | 0.461 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.460 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.460 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.460 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.459 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.459 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.458 | |
| 1zxn | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.458 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.458 | |
| 2dek | SAH | Diphthine synthase | / | 0.458 | |
| 2yy8 | SAM | tRNA (cytidine(56)-2'-O)-methyltransferase | / | 0.458 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.458 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.458 | |
| 4dx7 | DM2 | Multidrug efflux pump subunit AcrB | / | 0.458 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.458 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.457 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.457 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.456 | |
| 3r96 | ACO | MccE protein | / | 0.456 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.456 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.455 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.455 | |
| 2emu | SAH | Diphthine synthase | / | 0.454 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.454 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.454 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.454 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.454 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.454 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.453 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.453 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.453 | |
| 2ha8 | SAH | Probable methyltransferase TARBP1 | / | 0.453 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.453 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.453 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.452 | |
| 2dsg | SAH | Diphthine synthase | / | 0.452 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.452 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.452 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.452 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.452 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.451 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.451 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.451 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.451 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.451 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.451 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.451 | |
| 3uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.451 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.451 | |
| 4x3l | MTA | RNA 2'-O ribose methyltransferase | / | 0.451 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.451 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.450 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.450 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.450 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.450 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.449 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 2e15 | SAH | Diphthine synthase | / | 0.449 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.449 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.449 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.449 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.448 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.448 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1t8x | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.447 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.447 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.447 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.447 | |
| 3u9e | COA | Lmo1369 protein | / | 0.447 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.446 | |
| 2e16 | SAH | Diphthine synthase | / | 0.446 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.446 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.446 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.446 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.446 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.445 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2owv | SAH | Diphthine synthase | / | 0.445 | |
| 2pck | SAH | Diphthine synthase | / | 0.445 | |
| 3cop | ADP | Glycogen synthase | 2.4.1.21 | 0.445 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.445 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.444 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.444 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.444 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2xfy | ACX | Beta-amylase | 3.2.1.2 | 0.444 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.444 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.444 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.444 | |
| 4fdu | IHS | Putative multiple inositol polyphosphate histidine phosphatase 1 | / | 0.444 | |
| 1dj2 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.443 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.443 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.443 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.443 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.443 | |
| 3uu1 | 14B | Anthranilate phosphoribosyltransferase | / | 0.443 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.443 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 4e2d | FMN | Dehydrogenase | / | 0.443 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.443 | |
| 4qec | NAP | ElxO | / | 0.443 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.443 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.443 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.443 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.442 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.441 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.441 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.441 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.441 | |
| 3bbh | SFG | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 0.441 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.441 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.441 | |
| 3tdj | 3TJ | Glutamate receptor 2 | / | 0.441 | |
| 4brd | ANP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.441 | |
| 4cnf | MTA | SpoU rRNA methylase | / | 0.441 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.440 | |
| 1vce | SAH | Diphthine synthase | / | 0.440 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.440 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 2el0 | SAH | Diphthine synthase | / | 0.440 | |
| 2udp | UPP | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.440 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.440 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.440 | |
| 3lpf | Z77 | Beta-glucuronidase | 3.2.1.31 | 0.440 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.440 | |
| 4jic | FMN | GTN Reductase | / | 0.440 |