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 |
|---|---|---|---|
| 5exd | TPP | Oxalate oxidoreductase subunit alpha |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5exd | TPP | Oxalate oxidoreductase subunit alpha | / | 1.000 | |
| 5exd | TPP | Oxalate oxidoreductase subunit beta | / | 1.000 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit alpha | / | 0.569 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit beta | / | 0.569 | |
| 2c3p | 1TP | Pyruvate synthase | / | 0.540 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.533 | |
| 2uza | HTL | Pyruvate synthase | / | 0.529 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.518 | |
| 1qpb | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.508 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.501 | |
| 3tk0 | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.490 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.482 | |
| 3u5s | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.481 | |
| 2c3u | 2TP | Pyruvate synthase | / | 0.480 | |
| 2w93 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.480 | |
| 1kek | HTL | Pyruvate synthase | / | 0.479 | |
| 3cd5 | 7HI | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.479 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.478 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.477 | |
| 3otf | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.477 | |
| 2vk4 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.476 | |
| 2c3y | HTL | Pyruvate synthase | / | 0.474 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.473 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.470 | |
| 2y3r | TRK | TamL | / | 0.469 | |
| 2vk8 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.468 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.468 | |
| 3dle | GFA | Gag-Pol polyprotein | 2.7.7.49 | 0.466 | |
| 1ovm | TPP | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.465 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.465 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.465 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.464 | |
| 4e8y | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.464 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.463 | |
| 4asy | N5Y | Glucose-1-phosphate thymidylyltransferase | / | 0.462 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.461 | |
| 2pda | TPP | Pyruvate synthase | / | 0.461 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.461 | |
| 3qx2 | X63 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.460 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.459 | |
| 1u26 | IHS | Myo-inositol hexaphosphate phosphohydrolase | / | 0.458 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 4xzn | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.458 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.457 | |
| 4g3p | UD1 | Bifunctional protein GlmU | / | 0.457 | |
| 5dld | UD1 | UDP-N-Acetylglucosamine 2-epimerase | / | 0.457 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.457 | |
| 2c3o | TPP | Pyruvate synthase | / | 0.456 | |
| 3bpz | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | / | 0.456 | |
| 3q5k | D1U | Heat shock protein 83-1 | / | 0.456 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.456 | |
| 1r6g | 442 | Thyroid hormone receptor beta | / | 0.455 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.455 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.455 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.455 | |
| 3v49 | PK0 | Androgen receptor | / | 0.455 | |
| 2jib | TPP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.454 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.454 | |
| 1aiq | CB3 | Thymidylate synthase | / | 0.453 | |
| 1q43 | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | / | 0.453 | |
| 1rbq | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.453 | |
| 3eks | CY9 | Actin-5C | / | 0.453 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.453 | |
| 3sjz | GNP | Translation initiation factor 2 subunit gamma | / | 0.453 | |
| 3u2l | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.453 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.453 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.452 | |
| 2qg2 | A91 | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 3kga | LX9 | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.452 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 5dbv | COA | Aldehyde Dehydrogenase | / | 0.452 | |
| 1jsc | TPP | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.451 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.451 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 2cvv | ANP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.451 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.451 | |
| 3u9n | 09H | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.451 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.451 | |
| 1b3r | NAD | Adenosylhomocysteinase | 3.3.1.1 | 0.450 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.450 | |
| 3mbg | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.450 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.450 | |
| 4eil | CB3 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 1nas | ASE | Sepiapterin reductase | 1.1.1.153 | 0.449 | |
| 1s9d | AFB | Cytohesin-2 | / | 0.449 | |
| 1s9d | AFB | ADP-ribosylation factor 1 | / | 0.449 | |
| 1skg | VAL_ALA_PHE_ARG_SER | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.449 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.449 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.449 | |
| 4bqw | QNM | Egl nine homolog 1 | / | 0.449 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.449 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.449 | |
| 2cye | COA | Putative thioesterase | / | 0.448 | |
| 2py7 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.448 | |
| 2vwh | NAP | Glucose 1-dehydrogenase | / | 0.448 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.448 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.448 | |
| 4avl | TMP | Polymerase acidic protein | / | 0.448 | |
| 4e0h | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.448 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.448 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.447 | |
| 1rby | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.447 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.447 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.447 | |
| 2rr1 | W8R | Genome polyprotein | / | 0.447 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.447 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.447 | |
| 3rsr | N5P | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.447 | |
| 3zvv | XAZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 4er7 | AW3 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.447 | |
| 4n57 | ADP | APH(2'')-Id | / | 0.447 | |
| 4oav | ACP | 2-5A-dependent ribonuclease | 3.1.26 | 0.447 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.446 | |
| 1njs | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.446 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.446 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.446 | |
| 1u9i | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.446 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.446 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.446 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3s8c | ANP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.446 | |
| 4cym | GCP | Ras-related protein Rab-32 | / | 0.446 | |
| 4fsq | HK3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.446 | |
| 1in5 | ADP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.445 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.445 | |
| 1y8y | CT7 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 2ahv | COA | Acetate CoA-transferase YdiF | 2.8.3.8 | 0.445 | |
| 2c3l | IDZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.445 | |
| 2q7h | YLY | Pyrrolysine--tRNA ligase | / | 0.445 | |
| 3cd3 | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.445 | |
| 3cly | ACP | Fibroblast growth factor receptor 2 | / | 0.445 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 4awp | 99A | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.445 | |
| 4zhq | ACP | Tubulin tyrosine ligase | / | 0.445 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.445 | |
| 1chw | HXC | Chalcone synthase 2 | 2.3.1.74 | 0.444 | |
| 1p84 | UQ6 | Cytochrome b | / | 0.444 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 2c6k | DT2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 2jj1 | PIT | ATP synthase subunit alpha, mitochondrial | / | 0.444 | |
| 2jj1 | PIT | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.444 | |
| 2jj1 | PIT | ATP synthase subunit gamma, mitochondrial | / | 0.444 | |
| 2o0u | C0M | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.444 | |
| 2w6m | OA1 | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.444 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.444 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.444 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.444 | |
| 4f99 | ADP | Cell division cycle 7-related protein kinase | 2.7.11.1 | 0.444 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.444 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.444 | |
| 1e8x | ATP | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.443 | |
| 1ikv | EFZ | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 1svl | ADP | Large T antigen | 3.6.4 | 0.443 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.443 | |
| 2e08 | SAH | Diphthine synthase | / | 0.443 | |
| 3f8k | COA | Uncharacterized protein | / | 0.443 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 3r7c | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.443 | |
| 3u2m | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.443 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.443 | |
| 4an9 | 2P7 | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.443 | |
| 4ezl | 0SE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 4rrv | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.443 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.443 | |
| 4yvj | SFG | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.443 | |
| 1nsf | ATP | Vesicle-fusing ATPase | 3.6.4.6 | 0.442 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.442 | |
| 1os1 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.442 | |
| 1rc1 | KT3 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.442 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.442 | |
| 2bxf | DZP | Serum albumin | / | 0.442 | |
| 2daa | DCS | D-alanine aminotransferase | 2.6.1.21 | 0.442 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.442 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 3bc1 | GNP | Ras-related protein Rab-27A | / | 0.442 | |
| 3lfn | A27 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 3v4a | PK1 | Androgen receptor | / | 0.442 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.442 | |
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.442 | |
| 4cj4 | S3G | Integrase | / | 0.442 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.442 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.442 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.441 | |
| 1lny | IMO | Adenylosuccinate synthetase isozyme 1 | / | 0.441 | |
| 1nq1 | 4HY | Thyroid hormone receptor beta | / | 0.441 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.441 | |
| 2wmu | ZYU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2x4f | 16X | Myosin light chain kinase family member 4 | 2.7.11.1 | 0.441 | |
| 3kc0 | 2T5 | Fructose-1,6-bisphosphatase 1 | 3.1.3.11 | 0.441 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.441 | |
| 1lhw | ESM | Sex hormone-binding globulin | / | 0.440 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.440 | |
| 2e15 | SAH | Diphthine synthase | / | 0.440 | |
| 2ibz | UQ6 | Cytochrome b | / | 0.440 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.440 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 3evc | SAH | Genome polyprotein | 2.1.1.56 | 0.440 | |
| 3fc1 | 52P | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3iog | SDF | Metallo-beta-lactamase type 2 | / | 0.440 | |
| 3ka0 | MK3 | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.440 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.440 | |
| 3tm0 | ANP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.440 | |
| 3upf | 0BU | Polyprotein | / | 0.440 | |
| 3zmm | F9J | Tyrosine-protein kinase JAK2 | / | 0.440 | |
| 4cfd | S8Y | Integrase | / | 0.440 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.440 |