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 |
|---|---|---|---|
| 4ros | APR | Malate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4ros | APR | Malate dehydrogenase | / | 1.000 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.553 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.541 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.538 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.533 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.533 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.528 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.518 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.515 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.514 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.511 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.507 | |
| 4ajn | 88V | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.499 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.492 | |
| 4ajo | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.492 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.487 | |
| 1ib6 | NAD | Malate dehydrogenase | / | 0.483 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.480 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.479 | |
| 1emd | NAD | Malate dehydrogenase | / | 0.477 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.477 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.477 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.476 | |
| 4dx7 | DM2 | Multidrug efflux pump subunit AcrB | / | 0.476 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.475 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.474 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.472 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.470 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.467 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.466 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.466 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.465 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.465 | |
| 4ajj | 88R | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.465 | |
| 1sny | NAP | LD36273p | / | 0.463 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.463 | |
| 5a3b | APR | SIR2 family protein | / | 0.463 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.462 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.462 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.462 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.461 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.460 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.459 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.458 | |
| 1w48 | APC | NTPase P4 | / | 0.458 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.458 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.458 | |
| 1daa | PLP | D-alanine aminotransferase | 2.6.1.21 | 0.457 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.457 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.457 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.457 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.456 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.456 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.455 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.455 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.455 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.454 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.453 | |
| 1nbo | NAD | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.453 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.453 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.452 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.451 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.451 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.451 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.451 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.450 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 5dp2 | NAP | CurF | / | 0.450 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.449 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.449 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.449 | |
| 4fnc | HMU | G/T mismatch-specific thymine DNA glycosylase | 3.2.2.29 | 0.449 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.449 | |
| 1aj2 | 2PH | Dihydropteroate synthase | / | 0.448 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.448 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.448 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.447 | |
| 5a3c | NAD | SIR2 family protein | / | 0.447 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.447 | |
| 1qf5 | RPL | Adenylosuccinate synthetase | / | 0.446 | |
| 1r2j | FAD | FkbI | / | 0.446 | |
| 4el5 | D1M | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.446 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.445 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.445 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.445 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.445 | |
| 4dja | FAD | (6-4) photolyase | / | 0.445 | |
| 1c6y | MK1 | Protease | / | 0.444 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.444 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.444 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.444 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.444 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.443 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.443 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.443 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1yjq | NAP | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.442 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.442 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.442 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.442 | |
| 3alj | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.442 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.442 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.442 | |
| 4lht | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.442 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.442 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.441 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.441 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.441 | |
| 4kqw | NAP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.441 | |
| 4qq3 | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.441 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.441 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.440 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.440 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.440 | |
| 3hrc | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3v3m | 0EN | Replicase polyprotein 1a | 3.4.19.12 | 0.440 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.440 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.440 |