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 |
|---|---|---|---|
| 5jqb | IBP | Envelope glycoprotein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5jqb | IBP | Envelope glycoprotein | / | 1.000 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.485 | |
| 4k9u | 5AW | Cytochrome P450 3A4 | / | 0.472 | |
| 1tz8 | DES | Transthyretin | / | 0.469 | |
| 1kgj | FL8 | Transthyretin | / | 0.467 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.467 | |
| 3tdl | 11D | Serum albumin | / | 0.467 | |
| 3cgd | NAD | Coenzyme A disulfide reductase | / | 0.466 | |
| 2bx8 | AZQ | Serum albumin | / | 0.465 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.463 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.463 | |
| 3zep | 1NX | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.463 | |
| 1ie4 | T44 | Transthyretin | / | 0.460 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.460 | |
| 3orp | AGS | Serine/threonine protein kinase | / | 0.460 | |
| 3qgt | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.460 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 2e9c | B75 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.459 | |
| 2bxn | IDB | Serum albumin | / | 0.458 | |
| 1gii | 1PU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.457 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.457 | |
| 3cgo | JNO | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.456 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.455 | |
| 1ict | T44 | Transthyretin | / | 0.453 | |
| 1jvs | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.453 | |
| 2bxi | AZQ | Serum albumin | / | 0.453 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.453 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.453 | |
| 2vu3 | LZE | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.453 | |
| 4mvf | STU | Calcium-dependent protein kinase 2 | 2.7.11.1 | 0.453 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 3q4z | ANP | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.452 | |
| 3wec | AUI | Cytochrome P450 | / | 0.452 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4hge | 15V | Tyrosine-protein kinase JAK2 | / | 0.452 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.452 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.451 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.451 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.450 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 4awi | AQ2 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.450 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.449 | |
| 2wqe | ADP | Aurora kinase A | 2.7.11.1 | 0.449 | |
| 3at4 | CCK | Casein kinase II subunit alpha | 2.7.11.1 | 0.449 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.449 | |
| 4pd6 | URI | Nucleoside permease | / | 0.449 | |
| 4ysj | ADP | Calmodulin-like domain protein kinase | / | 0.449 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.448 | |
| 3efw | AK8 | Aurora kinase A | 2.7.11.1 | 0.448 | |
| 3gu7 | ADP | Death-associated protein kinase 1 | 2.7.11.1 | 0.448 | |
| 4bcm | T7Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 1b38 | ATP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.447 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.447 | |
| 4l3j | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.447 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.447 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2hnz | PC0 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 2j5n | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.446 | |
| 2zbz | VDX | Vitamin D3 dihydroxylase | / | 0.446 | |
| 3sgx | 0FW | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.446 | |
| 3vth | APC | Carbamoyltransferase | / | 0.446 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 4ix5 | ANP | Uncharacterized protein | / | 0.446 | |
| 4oj4 | DIF | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.446 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.445 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1sn5 | T3 | Transthyretin | / | 0.445 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.445 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.445 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 3vid | 4TT | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.445 | |
| 3vn9 | ANK | Dual specificity mitogen-activated protein kinase kinase 6 | 2.7.12.2 | 0.445 | |
| 3zux | TCH | Transporter | / | 0.445 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.445 | |
| 1tvr | TB9 | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.444 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.444 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.444 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.444 | |
| 2xvd | AS6 | Ephrin type-B receptor 4 | 2.7.10.1 | 0.444 | |
| 3cgf | JNF | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.444 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 4crs | AGS | Serine/threonine-protein kinase N2 | 2.7.11.13 | 0.444 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.444 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.443 | |
| 2izs | BRQ | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.443 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.443 | |
| 3fgo | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.443 | |
| 3hcr | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.443 | |
| 4g73 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.443 | |
| 4hjf | C2E | GGDEF family protein | / | 0.443 | |
| 1cbs | REA | Cellular retinoic acid-binding protein 2 | / | 0.442 | |
| 1osv | CHC | Bile acid receptor | / | 0.442 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.442 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.442 | |
| 4jbo | WPH | Aurora kinase A | 2.7.11.1 | 0.442 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.442 | |
| 4mcv | 29K | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.442 | |
| 4mq1 | 2C3 | Dual specificity tyrosine-phosphorylation-regulated kinase 1A | 2.7.12.1 | 0.442 | |
| 4qny | ANP | Mitogen activated protein kinase, putative | / | 0.442 | |
| 1dj3 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.441 | |
| 1g67 | TZP | Thiamine-phosphate synthase | / | 0.441 | |
| 1uyr | D1L | Acetyl-CoA carboxylase | / | 0.441 | |
| 2ycq | UPX | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.441 | |
| 3dfc | ANP | Death-associated protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3iqe | F42 | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.441 | |
| 3q30 | D61 | Squalene synthase | 2.5.1.21 | 0.441 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 4dta | ADN | APH(2'')-Id | / | 0.441 | |
| 4i3v | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.441 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.441 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.441 | |
| 5ap5 | 7RO | Dual specificity protein kinase TTK | 2.7.12.1 | 0.441 | |
| 1cbr | REA | Cellular retinoic acid-binding protein 1 | / | 0.440 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.440 | |
| 1rx5 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1sqv | UHD | Cytochrome b | / | 0.440 | |
| 2w4i | VGA | Glutamate racemase | / | 0.440 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.440 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3glm | COO | Glutaconyl-CoA decarboxylase alpha subunit | / | 0.440 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4ktf | 1TM | Cytochrome P450 | / | 0.440 |