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 |
|---|---|---|---|
| 1wdt | GTP | Elongation factor G (EF-G-2) |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1wdt | GTP | Elongation factor G (EF-G-2) | / | 1.000 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.535 | |
| 4o2r | GDP | GTP-binding protein Rheb | / | 0.487 | |
| 4j5r | A1R | O-acetyl-ADP-ribose deacetylase 1 | 3.5.1 | 0.485 | |
| 4g01 | GDP | Ras-related protein RABF2b | / | 0.483 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.482 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.481 | |
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 0.480 | |
| 1ky2 | GNP | GTP-binding protein YPT7 | / | 0.479 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.479 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.479 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.479 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.478 | |
| 3oog | YTP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.477 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.475 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.474 | |
| 1rj9 | GCP | Signal recognition particle receptor FtsY | / | 0.473 | |
| 2uzu | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.471 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.471 | |
| 2p2l | GDP | Ras-related C3 botulinum toxin substrate 1 | / | 0.469 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.469 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.469 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.468 | |
| 3k14 | 535 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.468 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.468 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.467 | |
| 3kkv | B99 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.467 | |
| 4aa5 | NQB | Mitogen-activated protein kinase 14 | / | 0.467 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.466 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.466 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.466 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.465 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.465 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.465 | |
| 2ic5 | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.465 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.465 | |
| 3iph | G11 | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 4fsr | HKC | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.465 | |
| 4iaf | ADP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.465 | |
| 1jay | F42 | F420-dependent NADP reductase | / | 0.464 | |
| 1uu9 | BI3 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.464 | |
| 2rc3 | NAD | CBS domain | / | 0.464 | |
| 4el5 | D1M | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.464 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.464 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.463 | |
| 4dxa | GSP | Ras-related protein Rap-1b | / | 0.463 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.462 | |
| 3ref | GDP | Rho family GTPase | / | 0.462 | |
| 1mei | MOA | Inosine-5'-monophosphate dehydrogenase | / | 0.461 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.461 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.460 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.460 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.460 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.460 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.459 | |
| 1mei | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.459 | |
| 2yvg | NAD | Ferredoxin reductase | / | 0.459 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.459 | |
| 4bi1 | ZO6 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.459 | |
| 4xnh | ACO | N-terminal acetyltransferase A complex subunit NAT5 | 2.3.1 | 0.459 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.458 | |
| 3fwr | ADP | Transcriptional repressor CcpN | / | 0.458 | |
| 3jvv | ACP | Twitching mobility protein | / | 0.458 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.458 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.458 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.458 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.458 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.457 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.457 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.457 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.457 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.457 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.457 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.456 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.456 | |
| 4xvr | GNP | GTPase HRas | / | 0.456 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.455 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.455 | |
| 4mq1 | 2C3 | Dual specificity tyrosine-phosphorylation-regulated kinase 1A | 2.7.12.1 | 0.455 | |
| 1okk | GCP | Signal recognition particle protein | / | 0.454 | |
| 1okk | GCP | Signal recognition particle receptor FtsY | / | 0.454 | |
| 2uzf | CAA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.454 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.453 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.453 | |
| 3tgp | GNP | GTPase HRas | / | 0.453 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.453 | |
| 4kwh | NAP | Reductase homolog | / | 0.453 | |
| 4q03 | GDP | GTPase KRas | / | 0.453 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.452 | |
| 1x14 | NAD | NAD(P) transhydrogenase subunit alpha | 1.6.1.2 | 0.452 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.452 | |
| 2f7z | 6EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.452 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.452 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.452 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.452 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.452 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.452 | |
| 1h48 | CDI | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.451 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.451 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1f28 | UMP | Thymidylate synthase | 2.1.1.45 | 0.450 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.450 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.450 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.450 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.450 | |
| 4b5b | BBE | Glucose-1-phosphate thymidylyltransferase | / | 0.450 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.450 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.450 | |
| 1am4 | GNP | Cell division control protein 42 homolog | / | 0.449 | |
| 1h47 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.449 | |
| 2bu2 | ATP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.449 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 2w06 | FRV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.449 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.449 | |
| 3o7l | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.449 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 4fg7 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.449 | |
| 5ftc | ADP | TPR domain protein | / | 0.449 | |
| 1bv9 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1h48 | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.448 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.448 | |
| 2ojj | 82A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.448 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.448 | |
| 3ogw | IMN | Lactoperoxidase | 1.11.1.7 | 0.448 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.448 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.448 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.448 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.448 | |
| 4luc | GDP | GTPase KRas | / | 0.448 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.447 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.447 | |
| 3bxz | ADP | Protein translocase subunit SecA | / | 0.447 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.447 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.447 | |
| 3r0i | C0K | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.447 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 5cb3 | APR | O-acetyl-ADP-ribose deacetylase | / | 0.447 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1emd | NAD | Malate dehydrogenase | / | 0.446 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.446 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.446 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.446 | |
| 3gxl | QIG | TGF-beta receptor type-1 | 2.7.11.30 | 0.446 | |
| 3mje | NDP | AmphB | / | 0.446 | |
| 3r4p | FU7 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.446 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.445 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.445 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.445 | |
| 4hbn | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.445 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.444 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.444 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.444 | |
| 1kol | NAD | Glutathione-independent formaldehyde dehydrogenase | / | 0.444 | |
| 1q4u | 4CA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.444 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.444 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.444 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.444 | |
| 4l4x | NDP | AmphI | / | 0.444 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.444 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.444 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 1qm5 | PLP | Maltodextrin phosphorylase | 2.4.1.1 | 0.443 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.443 | |
| 2uzh | CDP | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.443 | |
| 2xy9 | 3ES | Angiotensin-converting enzyme | 3.2.1 | 0.443 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4fog | C2F | Thymidylate synthase ThyA | / | 0.443 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.442 | |
| 1mes | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.442 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3fly | FLY | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3r4b | 74T | Gag-Pol polyprotein | / | 0.442 | |
| 4c4h | 7RO | Dual specificity protein kinase TTK | 2.7.12.1 | 0.442 | |
| 4ple | CPS | Nuclear receptor subfamily 5 group A member 2 | / | 0.442 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.442 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.442 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.442 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.441 | |
| 1yu9 | GNP | Ras-related protein Rab-4A | / | 0.441 | |
| 2hog | 710 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.441 | |
| 3nbw | TR4 | Ketohexokinase | / | 0.441 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.441 | |
| 3wt0 | ATP | Cell division protein FtsA | / | 0.441 | |
| 4dmg | SAM | Uncharacterized protein | / | 0.441 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.441 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.440 | |
| 2gu8 | 796 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2q29 | ACO | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.440 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.440 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.440 | |
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 3of4 | FMN | Nitroreductase | / | 0.440 | |
| 3q71 | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.440 | |
| 3r7w | GNP | GTP-binding protein GTR2 | / | 0.440 | |
| 3uwq | U5P | Orotidine 5'-phosphate decarboxylase | / | 0.440 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.440 | |
| 4fln | UNK_UNK_TRP_UNK | Protease Do-like 2, chloroplastic | 3.4.21 | 0.440 | |
| 4s34 | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.440 |