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 |
|---|---|---|---|
| 1czn | FMN | Flavodoxin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1czn | FMN | Flavodoxin | / | 1.000 | |
| 1ofv | FMN | Flavodoxin | / | 0.817 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.561 | |
| 2v5u | FMN | Flavodoxin | / | 0.559 | |
| 3hr4 | FMN | Nitric oxide synthase, inducible | 1.14.13.39 | 0.558 | |
| 1j9g | FMN | Flavodoxin | / | 0.537 | |
| 1c7f | FMN | Flavodoxin | / | 0.536 | |
| 1azl | FMN | Flavodoxin | / | 0.534 | |
| 1ahn | FMN | Flavodoxin 1 | / | 0.530 | |
| 3esy | FMN | Flavodoxin | / | 0.529 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.520 | |
| 1fx1 | FMN | Flavodoxin | / | 0.509 | |
| 1j8q | FMN | Flavodoxin | / | 0.509 | |
| 1wsb | FMN | Flavodoxin | / | 0.509 | |
| 2fcr | FMN | Flavodoxin | / | 0.509 | |
| 2v5v | FMN | Flavodoxin | / | 0.508 | |
| 5tgz | FMN | Cannabinoid receptor 1 | / | 0.508 | |
| 3f6r | FMN | Flavodoxin | / | 0.505 | |
| 2mok | FMN | Flavodoxin 1 | / | 0.501 | |
| 1akr | FMN | Flavodoxin | / | 0.500 | |
| 3kap | FMN | Flavodoxin | / | 0.500 | |
| 3esz | FMN | Flavodoxin | / | 0.496 | |
| 2fx2 | FMN | Flavodoxin | / | 0.495 | |
| 1akw | FMN | Flavodoxin | / | 0.494 | |
| 3f90 | FMN | Flavodoxin | / | 0.491 | |
| 1xqp | 8HG | N-glycosylase/DNA lyase | / | 0.487 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.487 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.484 | |
| 1aku | FMN | Flavodoxin | / | 0.483 | |
| 3n39 | FMN | Protein NrdI | / | 0.482 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.477 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 3nn6 | HNK | 6-hydroxy-L-nicotine oxidase | / | 0.475 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.475 | |
| 4fx2 | FMN | Flavodoxin | / | 0.475 | |
| 5xra | FMN | Cannabinoid receptor 1 | / | 0.475 | |
| 4n65 | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.474 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 5fx2 | FMN | Flavodoxin | / | 0.473 | |
| 1j9z | FMN | NADPH--cytochrome P450 reductase | / | 0.472 | |
| 1yob | FMN | Flavodoxin 2 | / | 0.472 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.470 | |
| 3anl | SYC | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.467 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.467 | |
| 3kaq | FMN | Flavodoxin | / | 0.466 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.464 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.464 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.464 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.463 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.463 | |
| 1bu5 | RBF | Flavodoxin | / | 0.462 | |
| 3ai0 | PNW | Beta-glucosidase | / | 0.462 | |
| 3eku | CY9 | Actin-5C | / | 0.462 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.462 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.462 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.461 | |
| 4uaj | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.461 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.460 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.460 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.459 | |
| 3g5i | DNB | Pyrimidine-specific ribonucleoside hydrolase RihA | / | 0.459 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.458 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.458 | |
| 5xr8 | FMN | Cannabinoid receptor 1 | / | 0.458 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.457 | |
| 3of3 | DIH | Purine nucleoside phosphorylase DeoD-type 1 | / | 0.457 | |
| 3w5u | FAD | Ferredoxin | / | 0.457 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.456 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 0.456 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.456 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.455 | |
| 1pfy | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.455 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.455 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.454 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.454 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1kux | CA3 | Serotonin N-acetyltransferase | / | 0.453 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.453 | |
| 3qfs | FAD | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 3v2u | ATP | Protein GAL3 | / | 0.453 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4ts9 | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.453 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.452 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.452 | |
| 1xyy | FMN | Flavodoxin | / | 0.452 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 2r8p | T6F | Transketolase 1 | / | 0.452 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.452 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.452 | |
| 1w87 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.451 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3n3a | FMN | Protein NrdI | / | 0.451 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.451 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.451 | |
| 4h2d | FMN | NADPH-dependent diflavin oxidoreductase 1 | / | 0.451 | |
| 4jxz | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.451 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.450 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.449 | |
| 1e6z | NGO | Chitinase | / | 0.449 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.449 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.449 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.449 | |
| 3gc4 | AAQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.449 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.449 | |
| 1owp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.448 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.448 | |
| 2onf | COA | Uncharacterized protein | / | 0.448 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.448 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.448 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.448 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.448 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.448 | |
| 4ug5 | H4B | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.448 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.447 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.447 | |
| 4u7w | NDP | MxaA | / | 0.447 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.447 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.446 | |
| 1gaq | FAD | Ferredoxin | / | 0.446 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.446 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.446 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.446 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.445 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.445 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.445 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.445 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.445 | |
| 3klb | FMN | Uncharacterized protein | / | 0.445 | |
| 3l7g | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.445 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1lgt | BP3 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.444 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4y6g | F6F | Tryptophan synthase alpha chain | / | 0.444 | |
| 1p4a | PCP | Pur operon repressor | / | 0.443 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.443 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.443 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.442 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.442 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.442 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.442 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4isu | IKM | Glutamate receptor 2 | / | 0.442 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.441 | |
| 1fue | FMN | Flavodoxin | / | 0.441 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.441 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.441 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 1xxj | UNC | Uricase | 1.7.3.3 | 0.440 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.440 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.440 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.440 | |
| 2qmz | LDP | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.440 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3e6e | DCS | Alanine racemase | / | 0.440 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.440 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.440 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.440 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.440 |