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 |
|---|---|---|---|
| 1sbz | FMN | Probable UbiX-like flavin prenyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1sbz | FMN | Probable UbiX-like flavin prenyltransferase | / | 1.000 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.478 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 4itx | IN5 | Cystathionine beta-lyase MetC | 4.4.1.8 | 0.474 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.469 | |
| 5k7w | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.469 | |
| 3dzi | RGT | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.468 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.467 | |
| 4bue | JQF | Tankyrase-2 | 2.4.2.30 | 0.467 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.464 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.464 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.464 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.464 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.461 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.461 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.460 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.460 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.460 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.458 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.455 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4bus | 32F | Tankyrase-2 | 2.4.2.30 | 0.455 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.455 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.455 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.453 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.453 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.453 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.453 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.452 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.452 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 2hzq | STR | Apolipoprotein D | / | 0.451 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.451 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.451 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.451 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.451 | |
| 4bux | F35 | Tankyrase-2 | 2.4.2.30 | 0.451 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.450 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.450 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.450 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.450 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.449 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.449 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.449 | |
| 2nr4 | FMN | Conserved protein | / | 0.449 | |
| 3buz | TAD | Iota toxin component Ia | / | 0.449 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.448 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.448 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.448 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.448 | |
| 4l2g | 1V4 | Tankyrase-2 | 2.4.2.30 | 0.448 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.447 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.447 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.447 | |
| 4g1f | 0WG | Dipeptidyl peptidase 4 | / | 0.447 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.446 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.446 | |
| 3p0p | NNF | Tankyrase-2 | 2.4.2.30 | 0.446 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.446 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1gm8 | SOX | Penicillin G acylase | 3.5.1.11 | 0.445 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.445 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.445 | |
| 4iif | CTS | Beta-glucosidase 1 | 3.2.1.21 | 0.445 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.445 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.444 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.444 | |
| 4hlh | 20D | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4l0v | 1V1 | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 2ejz | SAH | Diphthine synthase | / | 0.443 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.443 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.443 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.443 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.442 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.442 | |
| 4xul | GTP | Uncharacterized protein mg662 | / | 0.442 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.442 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2iml | FMN | Uncharacterized protein | / | 0.441 | |
| 2o3u | NGD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.441 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4kzl | 20D | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.440 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.440 |