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 |
|---|---|---|---|
| 1raa | CTP | Aspartate carbamoyltransferase regulatory chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1raa | CTP | Aspartate carbamoyltransferase regulatory chain | / | 1.000 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.492 | |
| 4de5 | 0JD | Pantothenate synthetase | 6.3.2.1 | 0.485 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.482 | |
| 1qpe | PP2 | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.481 | |
| 3h03 | UBP | Glutamate receptor 2 | / | 0.478 | |
| 1y8y | CT7 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.477 | |
| 4f1y | CNI | Glutamate receptor 3 | / | 0.475 | |
| 4y45 | F91 | Endothiapepsin | 3.4.23.22 | 0.475 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.474 | |
| 4b1u | LAB | Actin, alpha skeletal muscle | / | 0.474 | |
| 4gy2 | LAR | Actin, alpha skeletal muscle | / | 0.473 | |
| 1q7g | NHO | Homoserine dehydrogenase | 1.1.1.3 | 0.472 | |
| 2y85 | 137 | Phosphoribosyl isomerase A | 5.3.1.16 | 0.472 | |
| 2yvf | FAD | Ferredoxin reductase | / | 0.472 | |
| 3nun | JMZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.472 | |
| 4fv2 | EK5 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.472 | |
| 4nt0 | 3DU | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.471 | |
| 2e9n | 76A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.470 | |
| 2j3n | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.470 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.470 | |
| 4gkh | 0J9 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.470 | |
| 3adc | ANP | L-seryl-tRNA(Sec) kinase | 2.7.1.164 | 0.468 | |
| 3pi0 | F91 | Endothiapepsin | 3.4.23.22 | 0.466 | |
| 3ruq | ADP | Chaperonin | / | 0.465 | |
| 4io8 | 3FD | Heat shock 70 kDa protein 1B | / | 0.465 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.464 | |
| 3i4b | Z48 | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.464 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.464 | |
| 3py0 | SU9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.464 | |
| 2v00 | V15 | Endothiapepsin | 3.4.23.22 | 0.463 | |
| 2v51 | LAB | Actin, alpha skeletal muscle | / | 0.463 | |
| 4d79 | ATP | tRNA threonylcarbamoyladenosine dehydratase | 6.1 | 0.463 | |
| 1gp2 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.462 | |
| 2v8p | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.462 | |
| 1oqm | UD2 | Beta-1,4-galactosyltransferase 1 | / | 0.461 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.461 | |
| 3pm4 | F5N | Endothiapepsin | 3.4.23.22 | 0.461 | |
| 3pmu | F7L | Endothiapepsin | 3.4.23.22 | 0.461 | |
| 4a4q | UX9 | Pol protein | / | 0.461 | |
| 2qs1 | UB1 | Glutamate receptor ionotropic, kainate 1 | / | 0.460 | |
| 3buz | LAR | Actin, alpha skeletal muscle | / | 0.460 | |
| 3ex8 | AIF | Riboflavin biosynthesis protein RibD | 1.1.1.193 | 0.460 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.460 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.460 | |
| 3rus | ADP | Chaperonin | / | 0.460 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.460 | |
| 1q8w | M77 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.459 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.459 | |
| 4gst | GTD | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.459 | |
| 4h03 | LAR | Actin, alpha skeletal muscle | / | 0.459 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.459 | |
| 1y56 | ATP | Uncharacterized protein | / | 0.458 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.458 | |
| 5fs9 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.458 | |
| 3sjh | LAR | Actin, alpha skeletal muscle | / | 0.457 | |
| 2cjm | ATP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.456 | |
| 3tm0 | ANP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.456 | |
| 4h0y | LAR | Actin, alpha skeletal muscle | / | 0.456 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.455 | |
| 4bec | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.455 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.454 | |
| 2v52 | LAB | Actin, alpha skeletal muscle | / | 0.454 | |
| 3mvh | WFE | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.454 | |
| 3pb5 | F63 | Endothiapepsin | 3.4.23.22 | 0.454 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.454 | |
| 4e5h | 0N8 | Polymerase acidic protein | / | 0.454 | |
| 4l45 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.454 | |
| 1hpx | KNI | Gag-Pol polyprotein | / | 0.453 | |
| 3dzv | ADP | Hydroxyethylthiazole kinase | / | 0.453 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.453 | |
| 3pdt | ADP | Myosin heavy chain kinase A | 2.7.11.7 | 0.453 | |
| 3rga | ILD | Epoxide hydrolase LasB | 5.5.1 | 0.453 | |
| 4bk2 | FAD | Probable salicylate monooxygenase | / | 0.453 | |
| 4cw5 | FMN | DfnA | / | 0.453 | |
| 4l44 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.453 | |
| 4ug9 | 1EW | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.453 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 1rc1 | KT3 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.452 | |
| 2ahc | VNL | Chorismate pyruvate-lyase | / | 0.452 | |
| 2wtd | ZZK | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.452 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.452 | |
| 2c6m | DT5 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.451 | |
| 3zo4 | QWI | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 2uzu | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 3ckq | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.449 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 4ctk | SAM | Genome polyprotein | / | 0.449 | |
| 4jik | 1KO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 2gej | GDD | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.448 | |
| 3b3p | JI7 | Nitric oxide synthase, brain | 1.14.13.39 | 0.448 | |
| 3ebf | 332 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.448 | |
| 3r71 | X86 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 3sfu | RBV | Polyprotein | / | 0.448 | |
| 4h1m | 0YJ | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.448 | |
| 5jjr | SAH | Genome polyprotein | / | 0.448 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.448 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 1rfq | LAR | Actin, alpha skeletal muscle | / | 0.447 | |
| 2xvu | 9DN | Serum albumin | / | 0.447 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.447 | |
| 3r73 | X87 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.447 | |
| 1q4u | 4CA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.446 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.446 | |
| 2e9p | 77A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 2oh0 | 2PY | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 3e7m | AT2 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.446 | |
| 3fg2 | FAD | Putative rubredoxin reductase | / | 0.446 | |
| 4xcz | T3Q | Qdtf | / | 0.446 | |
| 1rej | B1L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 2jir | MGD | Periplasmic nitrate reductase | / | 0.445 | |
| 2v2v | V12 | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 3ely | SAH | Methyltransferase | / | 0.445 | |
| 3roy | 22Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 4a9u | A9U | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.445 | |
| 4lfg | IPE | Putative geranyltranstransferase | / | 0.445 | |
| 4nte | FAD | DepH | / | 0.445 | |
| 2czf | XMP | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.444 | |
| 2j2p | SC2 | Ficolin-2 | / | 0.444 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.444 | |
| 2nvk | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.444 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.444 | |
| 3qfb | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.444 | |
| 4ei7 | GDP | Plasmid replication protein RepX | / | 0.444 | |
| 4j56 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.444 | |
| 5fs8 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.444 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1q3q | ANP | Thermosome subunit alpha | / | 0.443 | |
| 1yro | GDU | Beta-1,4-galactosyltransferase 1 | / | 0.443 | |
| 2b1i | 93A | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.443 | |
| 2c5y | MTW | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.443 | |
| 3ulk | NDP | Ketol-acid reductoisomerase (NADP(+)) | / | 0.443 | |
| 4beb | ATP | Type I restriction enzyme EcoR124II R protein | 3.1.21.3 | 0.443 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.443 | |
| 1gil | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.442 | |
| 1o23 | UPG | Beta-1,4-galactosyltransferase 1 | / | 0.442 | |
| 1pf9 | ADP | 60 kDa chaperonin | / | 0.442 | |
| 2bts | U32 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2gr2 | APR | Ferredoxin reductase | / | 0.442 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3clt | FAD | Electron transfer flavoprotein subunit alpha | / | 0.442 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.442 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.442 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 4fvz | 4KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 4zvl | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.442 | |
| 1m9n | AMZ | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.441 | |
| 1onf | FAD | Glutathione reductase | 1.8.1.7 | 0.441 | |
| 1tqm | ANP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.441 | |
| 1ykr | 628 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2pbz | ATP | Uncharacterized protein | / | 0.441 | |
| 2w0h | FAD | Trypanothione reductase | / | 0.441 | |
| 3nyn | SGV | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.441 | |
| 4ftr | 5HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 1gsu | GTX | Glutathione S-transferase 2 | 2.5.1.18 | 0.440 | |
| 1ijj | LAR | Actin, alpha skeletal muscle | / | 0.440 | |
| 1vso | AT1 | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 2bpw | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2j9g | ANP | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 2vo0 | M03 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3h5n | ATP | MccB protein | / | 0.440 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.440 | |
| 4lv7 | ADP | Inositol-pentakisphosphate 2-kinase | 2.7.1.158 | 0.440 |