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 |
|---|---|---|---|
| 1xyv | FMN | Flavodoxin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1xyv | FMN | Flavodoxin | / | 1.000 | |
| 2fx2 | FMN | Flavodoxin | / | 0.625 | |
| 1akw | FMN | Flavodoxin | / | 0.586 | |
| 3kap | FMN | Flavodoxin | / | 0.584 | |
| 1fx1 | FMN | Flavodoxin | / | 0.575 | |
| 4fx2 | FMN | Flavodoxin | / | 0.569 | |
| 1azl | FMN | Flavodoxin | / | 0.567 | |
| 1j9g | FMN | Flavodoxin | / | 0.563 | |
| 1bu5 | RBF | Flavodoxin | / | 0.560 | |
| 5xra | FMN | Cannabinoid receptor 1 | / | 0.560 | |
| 3f6r | FMN | Flavodoxin | / | 0.559 | |
| 1wsb | FMN | Flavodoxin | / | 0.558 | |
| 1j8q | FMN | Flavodoxin | / | 0.551 | |
| 1xyy | FMN | Flavodoxin | / | 0.543 | |
| 5fx2 | FMN | Flavodoxin | / | 0.543 | |
| 5tgz | FMN | Cannabinoid receptor 1 | / | 0.542 | |
| 3kaq | FMN | Flavodoxin | / | 0.528 | |
| 1akr | FMN | Flavodoxin | / | 0.517 | |
| 1c7f | FMN | Flavodoxin | / | 0.508 | |
| 2fcr | FMN | Flavodoxin | / | 0.503 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.500 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.498 | |
| 1ykg | FMN | Sulfite reductase [NADPH] flavoprotein alpha-component | / | 0.494 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.492 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.491 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.490 | |
| 5xr8 | FMN | Cannabinoid receptor 1 | / | 0.489 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.486 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.484 | |
| 3jqr | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.483 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 0.479 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.475 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.474 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.473 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.472 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.472 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.470 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.470 | |
| 1aku | FMN | Flavodoxin | / | 0.467 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.467 | |
| 1fue | FMN | Flavodoxin | / | 0.465 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.465 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 3ipk | PMS | Surface protein adhesin | / | 0.465 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.465 | |
| 4oxx | FMN | Cindoxin | / | 0.465 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.464 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.463 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.463 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.463 | |
| 2r8p | T6F | Transketolase 1 | / | 0.462 | |
| 3w5u | FAD | Ferredoxin | / | 0.462 | |
| 1qk3 | 5GP | Hypoxanthine-guanine-xanthine phosphoribosyltransferase | 2.4.2.22 | 0.461 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.461 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.461 | |
| 1czn | FMN | Flavodoxin | / | 0.460 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.458 | |
| 4b1h | AR6 | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.458 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.458 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.457 | |
| 2mt9 | FMN | Flavodoxin 2 | / | 0.457 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.457 | |
| 2b5o | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.456 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.456 | |
| 5d0r | B1T | Adenylate cyclase type 10 | / | 0.456 | |
| 1gaq | FAD | Ferredoxin | / | 0.455 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.455 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.455 | |
| 2xls | NAP | Putative flavin-containing monooxygenase | / | 0.455 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.455 | |
| 4jtr | IZP | Aldo-keto reductase family 1 member C2 | / | 0.455 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.453 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.453 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.453 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.452 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.452 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.452 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.452 | |
| 1ahn | FMN | Flavodoxin 1 | / | 0.451 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.451 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.451 | |
| 1ofv | FMN | Flavodoxin | / | 0.451 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.450 | |
| 2mok | FMN | Flavodoxin 1 | / | 0.450 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 3v49 | PK0 | Androgen receptor | / | 0.450 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.450 | |
| 1dmw | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.449 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.449 | |
| 2ejz | SAH | Diphthine synthase | / | 0.449 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.449 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.449 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.448 | |
| 2f2s | COA | Acetyl-CoA acetyltransferase, mitochondrial | 2.3.1.9 | 0.448 | |
| 2zwa | SAH | tRNA wybutosine-synthesizing protein 4 | 2.1.1.290 | 0.448 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.448 | |
| 3f0a | ACO | Spermidine N(1)-acetyltransferase | / | 0.448 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.448 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.448 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.448 | |
| 2bpo | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.447 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.447 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.447 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.447 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3x2f | NAI | Adenosylhomocysteinase | / | 0.447 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.447 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.447 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.446 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.446 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.446 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.445 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.445 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.445 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.445 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.445 | |
| 1nqw | 5YL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.444 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.444 | |
| 3wtk | TH4 | Acetylcholine-binding protein | / | 0.444 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4bmp | FMN | Protein NrdI | / | 0.444 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.444 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.444 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1lrm | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.443 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.443 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.443 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.443 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.443 | |
| 4xj4 | 3AT | Cyclic GMP-AMP synthase | / | 0.443 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.442 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.442 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.442 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.442 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.442 | |
| 4e2y | JHZ | Methyltransferase | / | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.441 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.441 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.441 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 1lke | DOG | Bilin-binding protein | / | 0.440 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.440 | |
| 2e1z | B4P | Propionate kinase | / | 0.440 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.440 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3o73 | O73 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 3p0h | FSE | Putative tyrosyl-tRNA synthetase | / | 0.440 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.440 |