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 |
|---|---|---|---|
| 4jin | 1L7 | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site 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 | 0.532 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.512 | |
| 1zp9 | ATP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.493 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.489 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.483 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.483 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.482 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.479 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.476 | |
| 3eld | SFG | Methyltransferase | / | 0.473 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.470 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.469 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.469 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.468 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.467 | |
| 1kor | ANP | Argininosuccinate synthase | / | 0.467 | |
| 3i4b | Z48 | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.467 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.466 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.465 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.465 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.465 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.464 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.463 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 3ncz | 3NC | Rho-associated protein kinase 1 | 2.7.11.1 | 0.460 | |
| 3w0s | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.460 | |
| 2cgu | 3A3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.459 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.459 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.458 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.458 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.458 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.458 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 3qpv | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.457 | |
| 4fv3 | EK6 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.457 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.457 | |
| 4j95 | ACP | Fibroblast growth factor receptor 2 | / | 0.457 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 3jsk | AHZ | Thiamine thiazole synthase | / | 0.456 | |
| 4fv6 | E57 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.456 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.455 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.455 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.455 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.455 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.454 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 4fv1 | EK4 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.454 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.454 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1ppj | ANY | Cytochrome b | / | 0.453 | |
| 4fg8 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.453 | |
| 5cvf | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.453 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.452 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.452 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.452 | |
| 4mvf | STU | Calcium-dependent protein kinase 2 | 2.7.11.1 | 0.452 | |
| 2j0m | 4ST | Focal adhesion kinase 1 | 2.7.10.2 | 0.451 | |
| 2pau | D5M | 5'-deoxynucleotidase YfbR | / | 0.451 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4fg7 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.451 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.451 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.451 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.450 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.450 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.450 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.449 | |
| 2ves | GVR | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.449 | |
| 2wsi | FAD | FAD synthase | 2.7.7.2 | 0.449 | |
| 2yyu | C5P | Orotidine 5'-phosphate decarboxylase | / | 0.449 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.449 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.449 | |
| 4fv5 | EK9 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.449 | |
| 1xdp | ATP | Polyphosphate kinase | / | 0.448 | |
| 2e08 | SAH | Diphthine synthase | / | 0.448 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.448 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.448 | |
| 3qcx | 3Q2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 4y95 | 746 | Tyrosine-protein kinase | / | 0.448 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.448 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.447 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.447 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.447 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.447 | |
| 3hrf | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.447 | |
| 4dit | 0KD | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.447 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.446 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.446 | |
| 3a99 | ANP | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.446 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.446 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.446 | |
| 4ifc | ADP | Serine/threonine-protein kinase PRP4 homolog | 2.7.11.1 | 0.446 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.445 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.445 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 3d1y | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.445 | |
| 1jkl | ANP | Death-associated protein kinase 1 | 2.7.11.1 | 0.444 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.444 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 5c41 | ACP | Ribokinase | / | 0.444 | |
| 1m0b | 0ZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2j9g | ANP | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 2uzt | SS3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.443 | |
| 4dt9 | GMP | APH(2'')-Id | / | 0.443 | |
| 4iwq | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.443 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 1ivp | 1ZK | Gag-Pol polyprotein | / | 0.442 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 2cgv | 3B3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.442 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.442 | |
| 2owu | SAH | Diphthine synthase | / | 0.442 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.442 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.442 | |
| 4btj | ATP | Tau-tubulin kinase 1 | 2.7.11.1 | 0.442 | |
| 4im0 | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.442 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.441 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.441 | |
| 3hrc | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3if9 | FAD | Glycine oxidase | 1.4.3.19 | 0.441 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3r4b | 74T | Gag-Pol polyprotein | / | 0.441 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 3t7x | 4SH | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 4ct2 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4rqk | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 1kh2 | ATP | Argininosuccinate synthase | / | 0.440 | |
| 1ohr | 1UN | V-1 PROTEASE protein | / | 0.440 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.440 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.440 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.440 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 2rg6 | 287 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.440 | |
| 3d1x | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.440 | |
| 3oev | 3OE | Proteasome subunit beta type-5 | 3.4.25.1 | 0.440 | |
| 3oev | 3OE | Proteasome subunit beta type-6 | 3.4.25.1 | 0.440 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.440 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 4xye | NAD | Formate dehydrogenase | / | 0.440 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.440 | |
| 5ap7 | SVE | Dual specificity protein kinase TTK | 2.7.12.1 | 0.440 |