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 |
|---|---|---|---|
| 2pv7 | NAD | T-protein | 1.3.1.12 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2pv7 | NAD | T-protein | 1.3.1.12 | 1.000 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.480 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.477 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.476 | |
| 4kwh | NAP | Reductase homolog | / | 0.476 | |
| 4oti | MI1 | Serine/threonine-protein kinase N1 | / | 0.476 | |
| 3zok | NAD | 3-dehydroquinate synthase, chloroplastic | 4.2.3.4 | 0.475 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.472 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.471 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.470 | |
| 2czf | XMP | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.469 | |
| 2d4v | NAD | Isocitrate dehydrogenase [NADP] | / | 0.469 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.468 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.468 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.467 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.466 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 3we4 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.465 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.464 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.463 | |
| 2itn | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.462 | |
| 4ho9 | GDU | Glucose-1-phosphate thymidylyltransferase | / | 0.462 | |
| 4l44 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.462 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.461 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.461 | |
| 2j7t | 274 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.461 | |
| 3tea | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.461 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.461 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 3zew | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.460 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.460 | |
| 1h1w | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.459 | |
| 2xbj | XBJ | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.459 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.458 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.458 | |
| 2o12 | FMN | Chorismate synthase | / | 0.458 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.458 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.457 | |
| 2e9u | A25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 3v8w | 0G2 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.457 | |
| 5a3c | NAD | SIR2 family protein | / | 0.457 | |
| 2jdt | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.456 | |
| 3wbb | NAP | Meso-diaminopimelate D-dehydrogenase | / | 0.456 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.456 | |
| 1c70 | L75 | Protease | / | 0.455 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.455 | |
| 1t44 | ATP | Actin, alpha skeletal muscle | / | 0.455 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.455 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.455 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.455 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.455 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.454 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.453 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.453 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.453 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.453 | |
| 4bdh | WVI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.453 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.452 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 3flw | FLW | Mitogen-activated protein kinase 14 | / | 0.451 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.451 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.451 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.451 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.450 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1sgu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 2dq7 | STU | Tyrosine-protein kinase Fyn | 2.7.10.2 | 0.450 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.450 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.450 | |
| 2y3r | TIR | TamL | / | 0.450 | |
| 3eej | 53R | Uncharacterized protein | / | 0.450 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.450 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.450 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.450 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.449 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.449 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.449 | |
| 2izr | BRK | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.449 | |
| 2ojf | 4PY | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 2yn8 | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.449 | |
| 3p3e | 3P3 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.449 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 4bid | IE8 | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.449 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.448 | |
| 2zgz | GNP | Plasmid segregation protein ParM | / | 0.448 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.448 | |
| 4jq7 | KJQ | Epidermal growth factor receptor | 2.7.10.1 | 0.448 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.447 | |
| 1rby | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.447 | |
| 2brm | DFZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.447 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.447 | |
| 2oh0 | 2PY | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 3ort | AGS | Serine/threonine protein kinase | / | 0.447 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.447 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.446 | |
| 2j09 | FMN | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 2vz6 | FEF | Calcium/calmodulin-dependent protein kinase type II subunit alpha | 2.7.11.17 | 0.446 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 2ydi | YDI | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.446 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.446 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 3opd | HIE | Heat shock protein 83 | / | 0.446 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.446 | |
| 5dhh | DGW | Nociceptin receptor | / | 0.446 | |
| 1bl6 | SB6 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.445 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 1s22 | ATP | Actin, alpha skeletal muscle | / | 0.445 | |
| 3bkb | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.445 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 3t2v | KKJ | Peptidoglycan recognition protein 1 | / | 0.445 | |
| 4l3l | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.445 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.445 | |
| 5ack | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.445 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.444 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 1r2j | FAD | FkbI | / | 0.444 | |
| 1uu7 | BI2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.444 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.444 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.444 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.444 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.444 | |
| 3rnn | RNN | Glutamate receptor 2 | / | 0.444 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.444 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.444 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.443 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2ad5 | ADP | CTP synthase | / | 0.443 | |
| 2bik | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.443 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.443 | |
| 2eva | ADN | Mitogen-activated protein kinase kinase kinase 7 | 2.7.11.25 | 0.443 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2izu | P01 | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.443 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.443 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.443 | |
| 2wti | WTI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.443 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.443 | |
| 3clh | NAD | 3-dehydroquinate synthase | 4.2.3.4 | 0.443 | |
| 3k3b | ADP | Kinesin-like protein KIF11 | / | 0.443 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.443 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.443 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4fv8 | E63 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.443 | |
| 4hnf | 16W | Casein kinase I isoform delta | 2.7.11.1 | 0.443 | |
| 4i23 | 1C9 | Epidermal growth factor receptor | 2.7.10.1 | 0.443 | |
| 4l2i | FAD | Electron transfer flavoprotein alpha/beta-subunit | / | 0.443 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.443 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.443 | |
| 4yqf | GDP | Septin-9 | / | 0.443 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.442 | |
| 1q4t | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.442 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 3igo | ANP | Calmodulin-domain protein kinase 1, putative | / | 0.442 | |
| 3l8x | N4D | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3umo | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.442 | |
| 3vs3 | VSE | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.442 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.442 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.442 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.442 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.442 | |
| 4ysw | FAD | Xanthine dehydrogenase/oxidase | / | 0.442 | |
| 1h5r | THM | Glucose-1-phosphate thymidylyltransferase 1 | / | 0.441 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.441 | |
| 1t7j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1zrq | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.441 | |
| 2gej | GDD | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.441 | |
| 2pvl | P55 | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.441 | |
| 3ekx | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3orz | BI4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4dta | ADN | APH(2'')-Id | / | 0.441 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.441 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.440 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.440 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.440 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.440 | |
| 2pe1 | 517 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.440 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.440 | |
| 3otf | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.440 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 | |
| 4kba | 1QM | Casein kinase I isoform delta | 2.7.11.1 | 0.440 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.440 | |
| 5l3r | GCP | Cell division protein FtsY homolog, chloroplastic | / | 0.440 |