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 |
|---|---|---|---|
| 1t36 | ADP | Carbamoyl-phosphate synthase large chain |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1t36 | ADP | Carbamoyl-phosphate synthase large chain | / | 1.000 | |
| 1jdb | ADP | Carbamoyl-phosphate synthase large chain | / | 0.593 | |
| 4l9q | 9TP | Serum albumin | / | 0.482 | |
| 5ify | UMP | Glucose-1-phosphate thymidylyltransferase | / | 0.481 | |
| 1ivh | COS | Isovaleryl-CoA dehydrogenase, mitochondrial | 1.3.8.4 | 0.479 | |
| 2zsh | GA3 | Gibberellin receptor GID1A | 3 | 0.478 | |
| 4mv3 | ACP | Biotin carboxylase | 6.3.4.14 | 0.476 | |
| 1pk8 | ATP | Synapsin-1 | / | 0.472 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.472 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.471 | |
| 3wo0 | ADP | Alanine--anticapsin ligase | / | 0.471 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.470 | |
| 1g4p | FQP | Thiamine-phosphate synthase | / | 0.469 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.469 | |
| 1nd5 | 2BF | Prostatic acid phosphatase | 3.1.3.2 | 0.468 | |
| 1tez | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.468 | |
| 3wo1 | ADP | Alanine--anticapsin ligase | / | 0.468 | |
| 4ma6 | 28E | Ara h 8 allergen | / | 0.468 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.467 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.467 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.466 | |
| 2yx6 | ADP | Uncharacterized protein | / | 0.465 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.465 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.464 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.463 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.462 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.462 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.461 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.461 | |
| 4f5d | C2E | Stimulator of interferon genes protein | / | 0.461 | |
| 5bpf | ADP | D-alanine--D-alanine ligase | / | 0.461 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.460 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.459 | |
| 2wpw | ACO | Orf14 | / | 0.459 | |
| 4qbh | AP5 | Adenylate kinase | / | 0.459 | |
| 1h9z | RWF | Serum albumin | / | 0.458 | |
| 3hz1 | 37D | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 4ho4 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.458 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.458 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 1eyn | 2AN | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.457 | |
| 2cvu | ANP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.457 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.457 | |
| 1xjn | DTP | Vitamin B12-dependent ribonucleotide reductase | / | 0.456 | |
| 2cvy | TTP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.456 | |
| 3wnz | ADP | Alanine--anticapsin ligase | / | 0.456 | |
| 1g4s | TPS | Thiamine-phosphate synthase | / | 0.455 | |
| 4d96 | 5PA | D-cysteine desulfhydrase | / | 0.455 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.455 | |
| 1a9x | ADP | Carbamoyl-phosphate synthase large chain | / | 0.454 | |
| 1ir3 | ANP | Insulin receptor | 2.7.10.1 | 0.454 | |
| 4ysw | NAI | Xanthine dehydrogenase/oxidase | / | 0.454 | |
| 3o15 | 3NM | Thiamine-phosphate synthase | / | 0.453 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.453 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.453 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.453 | |
| 1s4e | ADP | Galactokinase | / | 0.452 | |
| 4d9e | LCS | D-cysteine desulfhydrase | / | 0.452 | |
| 4l3l | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.452 | |
| 1uy6 | PU3 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 1uyf | PU1 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.451 | |
| 4eft | EFT | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 1g0r | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.450 | |
| 1q97 | ATP | Serine/threonine-protein kinase SKY1 | 2.7.11.1 | 0.450 | |
| 1yjq | NAP | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.450 | |
| 3f5u | ANP | Death-associated protein kinase 1 | 2.7.11.1 | 0.450 | |
| 3v1s | 0LH | Strictosidine synthase | 4.3.3.2 | 0.450 | |
| 3x04 | GNP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.450 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.450 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1g69 | TZP | Thiamine-phosphate synthase | / | 0.449 | |
| 1g6c | IFP | Thiamine-phosphate synthase | / | 0.449 | |
| 1h6v | NDP | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.449 | |
| 1qax | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.449 | |
| 2bxq | IMN | Serum albumin | / | 0.449 | |
| 2ijm | ATP | Focal adhesion kinase 1 | 2.7.10.2 | 0.449 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
| 4iqk | IQK | Kelch-like ECH-associated protein 1 | / | 0.449 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.448 | |
| 2vpy | MGD | Thiosulfate reductase | / | 0.448 | |
| 3qdd | 94M | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 4bqg | 50Q | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 2bpo | NAP | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.447 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.447 | |
| 4iyg | 1HU | Strictosidine synthase | 4.3.3.2 | 0.447 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.447 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.446 | |
| 1ouk | 084 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 2bxi | AZQ | Serum albumin | / | 0.446 | |
| 3cvu | FAD | RE11660p | / | 0.446 | |
| 1orr | CDP | CDP-paratose 2-epimerase | / | 0.445 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.445 | |
| 3gg0 | FMN | Uncharacterized protein | / | 0.445 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.445 | |
| 3mn7 | ATP | Actin-5C | / | 0.445 | |
| 4n49 | MGT | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 | 2.1.1.57 | 0.445 | |
| 1i58 | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.444 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.444 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.444 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.444 | |
| 4u7w | NDP | MxaA | / | 0.444 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.443 | |
| 1pvo | ANP | Transcription termination factor Rho | 3.6.4 | 0.443 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 1xje | TTP | Vitamin B12-dependent ribonucleotide reductase | / | 0.443 | |
| 2bun | FAD | AppA protein | / | 0.443 | |
| 3a13 | CAP | Ribulose bisphosphate carboxylase | / | 0.443 | |
| 3g8a | SAH | Ribosomal RNA small subunit methyltransferase G | / | 0.443 | |
| 3l05 | SN0 | N-acetylornithine carbamoyltransferase | 2.1.3.9 | 0.443 | |
| 3pcf | FHB | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.443 | |
| 3qlx | QLR | Uncharacterized protein | / | 0.443 | |
| 3r33 | 6ME | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3s87 | DGT | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.443 | |
| 4ag9 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.443 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4kq2 | 1S3 | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.443 | |
| 4n57 | ADP | APH(2'')-Id | / | 0.443 | |
| 1g9c | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.442 | |
| 1jra | FAD | FAD-linked sulfhydryl oxidase ERV2 | 1.8.3.2 | 0.442 | |
| 1jvs | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.442 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 2x60 | GTP | Mannose-1-phosphate guanylyltransferase | / | 0.442 | |
| 3o15 | IFP | Thiamine-phosphate synthase | / | 0.442 | |
| 4die | C5P | Cytidylate kinase | / | 0.442 | |
| 4dqw | ATP | Inosine-5'-monophosphate dehydrogenase | / | 0.442 | |
| 4ekk | ANP | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.442 | |
| 1mk1 | APR | MutT/nudix family protein | / | 0.441 | |
| 2eck | ADP | Adenylate kinase | / | 0.441 | |
| 2od7 | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.441 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3clb | TMQ | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3dj4 | UD1 | Bifunctional protein GlmU | / | 0.441 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.441 | |
| 3sa0 | NRA | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.441 | |
| 4g3p | UD1 | Bifunctional protein GlmU | / | 0.441 | |
| 4kq2 | U5P | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.441 | |
| 4xli | 1N1 | Abelson tyrosine-protein kinase 2 | 2.7.10.2 | 0.441 | |
| 1ebl | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.440 | |
| 1g67 | TZP | Thiamine-phosphate synthase | / | 0.440 | |
| 1wzy | F29 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.440 | |
| 2yej | XQK | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 2yej | ZZ3 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.440 | |
| 3eej | 53R | Uncharacterized protein | / | 0.440 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.440 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.440 | |
| 3u2x | ASO | Glycogenin-1 | 2.4.1.186 | 0.440 | |
| 3u5s | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.440 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4nt0 | 3DU | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.440 | |
| 4o1p | ANP | Ribonuclease L | / | 0.440 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.440 |