sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1czn | FMN | Flavodoxin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1czn | FMN | Flavodoxin | / | 1.000 | |
| 1ofv | FMN | Flavodoxin | / | 0.817 | |
| 3hr4 | FMN | Nitric oxide synthase, inducible | 1.14.13.39 | 0.590 | |
| 2v5u | FMN | Flavodoxin | / | 0.587 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.562 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.539 | |
| 1c7f | FMN | Flavodoxin | / | 0.537 | |
| 1j9g | FMN | Flavodoxin | / | 0.537 | |
| 1azl | FMN | Flavodoxin | / | 0.534 | |
| 3esy | FMN | Flavodoxin | / | 0.531 | |
| 1ahn | FMN | Flavodoxin 1 | / | 0.530 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.520 | |
| 5tgz | FMN | Cannabinoid receptor 1 | / | 0.510 | |
| 1fx1 | FMN | Flavodoxin | / | 0.509 | |
| 1j8q | FMN | Flavodoxin | / | 0.509 | |
| 1wsb | FMN | Flavodoxin | / | 0.509 | |
| 2fcr | FMN | Flavodoxin | / | 0.509 | |
| 3f90 | FMN | Flavodoxin | / | 0.509 | |
| 2v5v | FMN | Flavodoxin | / | 0.508 | |
| 3f6r | FMN | Flavodoxin | / | 0.506 | |
| 1akr | FMN | Flavodoxin | / | 0.505 | |
| 2mok | FMN | Flavodoxin 1 | / | 0.501 | |
| 3esz | FMN | Flavodoxin | / | 0.500 | |
| 3kap | FMN | Flavodoxin | / | 0.500 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.497 | |
| 1akw | FMN | Flavodoxin | / | 0.495 | |
| 2fx2 | FMN | Flavodoxin | / | 0.495 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.493 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.491 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.488 | |
| 3n39 | FMN | Protein NrdI | / | 0.488 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.487 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.487 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.484 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.484 | |
| 3f6s | FMN | Flavodoxin | / | 0.484 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.484 | |
| 1aku | FMN | Flavodoxin | / | 0.483 | |
| 1j9z | FMN | NADPH--cytochrome P450 reductase | / | 0.482 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.482 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.480 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.477 | |
| 4fx2 | FMN | Flavodoxin | / | 0.475 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.475 | |
| 5xra | FMN | Cannabinoid receptor 1 | / | 0.475 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 5fx2 | FMN | Flavodoxin | / | 0.473 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.472 | |
| 1yob | FMN | Flavodoxin 2 | / | 0.472 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.472 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.472 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.470 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.470 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.469 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.468 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.468 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.468 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.467 | |
| 4uaj | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.467 | |
| 1xqp | 8HG | N-glycosylase/DNA lyase | / | 0.466 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.466 | |
| 3kaq | FMN | Flavodoxin | / | 0.466 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 3ai0 | PNW | Beta-glucosidase | / | 0.465 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.464 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.464 | |
| 1bu5 | RBF | Flavodoxin | / | 0.463 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.463 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.463 | |
| 3eku | CY9 | Actin-5C | / | 0.462 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.462 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.462 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4ts9 | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.462 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.461 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.461 | |
| 3nn6 | HNK | 6-hydroxy-L-nicotine oxidase | / | 0.461 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.460 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.460 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.459 | |
| 5xr8 | FMN | Cannabinoid receptor 1 | / | 0.459 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.458 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.458 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.458 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.457 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 0.457 | |
| 3w5u | FAD | Ferredoxin | / | 0.457 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4qoh | STL | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.457 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 3of3 | DIH | Purine nucleoside phosphorylase DeoD-type 1 | / | 0.456 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.456 | |
| 1pfy | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.455 | |
| 3bus | SAH | Demethylrebeccamycin-D-glucose O-methyltransferase | / | 0.455 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.455 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.455 | |
| 5aqz | SGV | Heat shock 70 kDa protein 1A | / | 0.455 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.454 | |
| 1kux | CA3 | Serotonin N-acetyltransferase | / | 0.454 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.454 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.454 | |
| 3anl | SYC | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.454 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.454 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.454 | |
| 1owp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.453 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1xyy | FMN | Flavodoxin | / | 0.453 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.453 | |
| 3n3a | FMN | Protein NrdI | / | 0.453 | |
| 3qfs | FAD | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4bmp | FMN | Protein NrdI | / | 0.452 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1w87 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.451 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.451 | |
| 2pia | FMN | Phthalate dioxygenase reductase | / | 0.451 | |
| 2r8p | T6F | Transketolase 1 | / | 0.451 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.451 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.451 | |
| 4h2d | FMN | NADPH-dependent diflavin oxidoreductase 1 | / | 0.451 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.450 | |
| 2qmz | LDP | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.450 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.450 | |
| 3gc4 | AAQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.450 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.450 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.450 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.450 | |
| 4u7w | NDP | MxaA | / | 0.450 | |
| 1a69 | FMB | Purine nucleoside phosphorylase DeoD-type | / | 0.449 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.449 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 0.449 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.449 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.449 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.449 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 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 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.448 | |
| 3l7g | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.448 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3v2u | ATP | Protein GAL3 | / | 0.448 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.448 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.447 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.447 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.447 | |
| 3q7j | FBO | Tricorn protease-interacting factor F3 | 3.4.11 | 0.447 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.447 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.447 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.446 | |
| 1gaq | FAD | Ferredoxin | / | 0.446 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.446 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.446 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4bup | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.446 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.445 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.445 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.445 | |
| 3klb | FMN | Uncharacterized protein | / | 0.445 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.444 | |
| 1xmm | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.444 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.444 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3juo | AJD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.444 | |
| 4a6a | TTP | dCTP deaminase | 3.5.4.13 | 0.444 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.443 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.443 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.443 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.442 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.442 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.442 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.442 | |
| 3uq9 | TBN | Putative adenosine kinase | / | 0.442 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.442 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4ca8 | 3ES | Angiotensin-converting enzyme | 3.4.15.1 | 0.442 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.442 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.441 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 1fue | FMN | Flavodoxin | / | 0.441 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.441 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.441 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4n65 | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.441 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.441 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 1bdu | DUR | Thymidylate synthase | / | 0.440 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.440 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3bt9 | DEQ | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.440 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.440 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.440 |