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 |
|---|---|---|---|
| 1ykg | FMN | Sulfite reductase [NADPH] flavoprotein alpha-component |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1ykg | FMN | Sulfite reductase [NADPH] flavoprotein alpha-component | / | 1.000 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.500 | |
| 1akw | FMN | Flavodoxin | / | 0.494 | |
| 4h2d | FMN | NADPH-dependent diflavin oxidoreductase 1 | / | 0.491 | |
| 1bu5 | RBF | Flavodoxin | / | 0.489 | |
| 1yob | FMN | Flavodoxin 2 | / | 0.488 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.479 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.476 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.475 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.474 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 4rww | 2BA | Lmo2692 protein | / | 0.470 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.465 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.464 | |
| 1fue | FMN | Flavodoxin | / | 0.463 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.463 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.462 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.460 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.460 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.458 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 1zw1 | TN5 | Enoyl-ACP reductase | / | 0.456 | |
| 3f6r | FMN | Flavodoxin | / | 0.456 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.455 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.455 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.455 | |
| 3pdn | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.455 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.454 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.454 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.454 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.453 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1fx1 | FMN | Flavodoxin | / | 0.451 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 1l2t | ATP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.451 | |
| 1np7 | FAD | Cryptochrome DASH | / | 0.451 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3tif | ADP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.451 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.451 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.450 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.450 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.449 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.449 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.449 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.449 | |
| 1azl | FMN | Flavodoxin | / | 0.448 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.448 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.448 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.447 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.447 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.447 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.447 | |
| 3otf | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.446 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.445 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.445 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2ejz | SAH | Diphthine synthase | / | 0.445 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.445 | |
| 2bxm | IMN | Serum albumin | / | 0.444 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3reo | SAH | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.444 | |
| 3w2f | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.444 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.443 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.443 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3fnh | JPJ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.442 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.442 | |
| 2v2v | V12 | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.442 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.441 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.441 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.441 | |
| 3gon | ANP | Phosphomevalonate kinase | / | 0.441 | |
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase | / | 0.441 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1i5e | U5P | Uracil phosphoribosyltransferase | / | 0.440 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.440 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.440 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.440 | |
| 2y3p | SM8 | DNA gyrase subunit A | / | 0.440 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.440 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4e32 | DWN | Methyltransferase | / | 0.440 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.440 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 |