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 |
|---|---|---|---|
| 4jin | 1L7 | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4jin | 1L7 | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 1.000 | |
| 1ztf | XYA | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.567 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.486 | |
| 1zp9 | ATP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.483 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.479 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.478 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.477 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.472 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.468 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.468 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.468 | |
| 3ofm | 4B0 | Casein kinase II subunit alpha' | 2.7.11.1 | 0.468 | |
| 2cke | IQU | Death-associated protein kinase 2 | / | 0.467 | |
| 3eld | SFG | Methyltransferase | / | 0.467 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.467 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.464 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.464 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.464 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 4mvf | STU | Calcium-dependent protein kinase 2 | 2.7.11.1 | 0.463 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.461 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.460 | |
| 1q5k | TMU | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.459 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.459 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.458 | |
| 3gu8 | 3GU | Death-associated protein kinase 1 | 2.7.11.1 | 0.458 | |
| 2cgu | 3A3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.457 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.456 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.456 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4dit | 0KD | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.456 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.455 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 4fv3 | EK6 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.454 | |
| 4hge | 15V | Tyrosine-protein kinase JAK2 | / | 0.454 | |
| 1fvv | 107 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 3ncz | 3NC | Rho-associated protein kinase 1 | 2.7.11.1 | 0.453 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.453 | |
| 4lrz | ADP | PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.453 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.452 | |
| 4nk9 | 2K5 | Fibroblast growth factor receptor 1 | / | 0.452 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.451 | |
| 3at4 | CCK | Casein kinase II subunit alpha | 2.7.11.1 | 0.451 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.451 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.451 | |
| 3w0s | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.451 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4l7s | G7K | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.451 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.450 | |
| 2cmw | OLP | Casein kinase I isoform gamma-1 | 2.7.11.1 | 0.450 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.450 | |
| 4dta | ADN | APH(2'')-Id | / | 0.450 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.449 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.449 | |
| 2vv9 | IM9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.449 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.449 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2j0m | 4ST | Focal adhesion kinase 1 | 2.7.10.2 | 0.448 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.447 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 1qr6 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.447 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.447 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.447 | |
| 4fv6 | E57 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.447 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.446 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3my5 | RFZ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.446 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.445 | |
| 2w1f | L0F | Aurora kinase A | 2.7.11.1 | 0.445 | |
| 2yyu | C5P | Orotidine 5'-phosphate decarboxylase | / | 0.445 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.445 | |
| 4fg7 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.445 | |
| 4fv5 | EK9 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.445 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.445 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 3i4b | Z48 | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.444 | |
| 2e08 | SAH | Diphthine synthase | / | 0.443 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.443 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.443 | |
| 3qpv | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.443 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.443 | |
| 4aqc | 88A | Tyrosine-protein kinase JAK2 | / | 0.443 | |
| 4fv1 | EK4 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.443 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.443 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.443 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.442 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.442 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.442 | |
| 4f65 | 0S9 | Fibroblast growth factor receptor 1 | / | 0.442 | |
| 4fg8 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.442 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.442 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.441 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 2j9g | ANP | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 2uzt | SS3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.441 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2izu | P01 | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.440 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.440 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.440 | |
| 3rak | 03Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4grb | 0XG | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 4o0w | ADN | Aurora kinase A | 2.7.11.1 | 0.440 | |
| 5dt0 | SKE | Aurora kinase A | 2.7.11.1 | 0.440 |