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 |
|---|---|---|---|
| 1h5t | TYD | Glucose-1-phosphate thymidylyltransferase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1h5t | TYD | Glucose-1-phosphate thymidylyltransferase 1 | / | 1.000 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.593 | |
| 5ify | UMP | Glucose-1-phosphate thymidylyltransferase | / | 0.580 | |
| 4ho4 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.555 | |
| 1g0r | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.546 | |
| 4asy | N5Y | Glucose-1-phosphate thymidylyltransferase | / | 0.546 | |
| 1fxo | TMP | Glucose-1-phosphate thymidylyltransferase | / | 0.536 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.530 | |
| 4ho9 | UTP | Glucose-1-phosphate thymidylyltransferase | / | 0.509 | |
| 4b42 | 942 | Glucose-1-phosphate thymidylyltransferase | / | 0.495 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.494 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.486 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.485 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.483 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.479 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.478 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.476 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.476 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.475 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.475 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.475 | |
| 2w98 | P1Z | Prostaglandin reductase 2 | 1.3.1.48 | 0.472 | |
| 4b2w | BZ0 | Glucose-1-phosphate thymidylyltransferase | / | 0.472 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.472 | |
| 4asj | N6A | Glucose-1-phosphate thymidylyltransferase | / | 0.471 | |
| 1dj3 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.470 | |
| 2xb5 | I7T | Tetracycline repressor protein class D | / | 0.468 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.465 | |
| 3m9v | TYD | FAD-dependent oxidoreductase | / | 0.465 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 5fkm | TDC | Tetracycline repressor protein class D | / | 0.464 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.463 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.461 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.461 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.461 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.461 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.461 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.460 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.460 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 4b5b | BBE | Glucose-1-phosphate thymidylyltransferase | / | 0.460 | |
| 4bbh | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.459 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.459 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.459 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.459 | |
| 2vkv | TDC | Tetracycline repressor protein class D | / | 0.459 | |
| 1pxx | DIF | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.458 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.458 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.458 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.458 | |
| 1iqr | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.457 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.457 | |
| 2xrl | DXT | Tetracycline repressor protein class D | / | 0.457 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.457 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.457 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.457 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.457 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.456 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.456 | |
| 2wsa | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 4dij | BLF | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.456 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.456 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 2gej | GDD | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.455 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.455 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.455 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.455 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.454 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.454 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.454 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.454 | |
| 4b4b | GJB | Glucose-1-phosphate thymidylyltransferase | / | 0.454 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.454 | |
| 4xiv | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.454 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.453 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.453 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.453 | |
| 1g4p | FQP | Thiamine-phosphate synthase | / | 0.452 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.452 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.452 | |
| 3cop | ADP | Glycogen synthase | 2.4.1.21 | 0.452 | |
| 3sai | 9DR | Dihydrofolate reductase | / | 0.452 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.452 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.452 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.451 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.451 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.451 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.450 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.450 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.450 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.450 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.450 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 4lx9 | ACO | N-alpha-acetyltransferase | 2.3.1 | 0.450 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.450 | |
| 5fkn | TDC | Tetracycline repressor protein class D | / | 0.450 | |
| 1owm | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.449 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.449 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.449 | |
| 4ifn | 12O | Kelch-like ECH-associated protein 1 | / | 0.449 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.449 | |
| 5kf1 | ACO | Predicted acetyltransferase | / | 0.449 | |
| 1l7e | NAI | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.448 | |
| 1x8v | ESL | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.448 | |
| 2bgj | FAD | NADPH:ferredoxin reductase | / | 0.448 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.448 | |
| 3lj3 | WYE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1g6c | TZP | Thiamine-phosphate synthase | / | 0.447 | |
| 1q97 | ATP | Serine/threonine-protein kinase SKY1 | 2.7.11.1 | 0.447 | |
| 1u5r | ATP | Serine/threonine-protein kinase TAO2 | 2.7.11.1 | 0.447 | |
| 1zp9 | ATP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.447 | |
| 3ofm | 4B0 | Casein kinase II subunit alpha' | 2.7.11.1 | 0.447 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 3r35 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.447 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.447 | |
| 4b4g | KKT | Glucose-1-phosphate thymidylyltransferase | / | 0.447 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.447 | |
| 4kp5 | E1F | Carbonic anhydrase 12 | 4.2.1.1 | 0.447 | |
| 4l3l | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.447 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.447 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.446 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.446 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.446 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.446 | |
| 3vgl | ANP | Glucokinase | / | 0.446 | |
| 3wow | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.446 | |
| 4o0w | ADN | Aurora kinase A | 2.7.11.1 | 0.446 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.445 | |
| 1i7l | ATP | Synapsin-2 | / | 0.445 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.445 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 3g6w | GTP | Uracil phosphoribosyltransferase | 2.4.2.9 | 0.445 | |
| 4otp | ADP | Serine/threonine-protein kinase RIO1 | 2.7.11.1 | 0.445 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.445 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.445 | |
| 1cx2 | S58 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.444 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.444 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.444 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ydf | IO3 | Serum albumin | / | 0.444 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.444 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.444 | |
| 4p6w | MOF | Glucocorticoid receptor | / | 0.444 | |
| 1sn0 | T44 | Transthyretin | / | 0.443 | |
| 1t1s | CBQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.443 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.443 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.443 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.443 | |
| 3ln1 | CEL | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.443 | |
| 3lu7 | IPX | Serum albumin | / | 0.443 | |
| 3pjt | C2E | Diguanylate cyclase/phosphodiesterase | / | 0.443 | |
| 3tea | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.443 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.443 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.443 | |
| 4kcf | AKM | FAD-dependent oxidoreductase | / | 0.443 | |
| 4lnk | ADP | Glutamine synthetase | 6.3.1.2 | 0.443 | |
| 4m99 | ACO | UDP-N-acetylgalactosaminyltransferase | / | 0.443 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.443 | |
| 5kjf | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 1qxo | FMN | Chorismate synthase | / | 0.442 | |
| 1tdu | CB3 | Thymidylate synthase | / | 0.442 | |
| 2j7t | 274 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.442 | |
| 2r4t | ADP | Glycogen synthase | 2.4.1.21 | 0.442 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.442 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.442 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.442 | |
| 4f6w | 0SS | Cyclin-dependent kinase 8 | 2.7.11.22 | 0.442 | |
| 4ix5 | ANP | Uncharacterized protein | / | 0.442 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.442 | |
| 5bn3 | ADP | NEQ263 | / | 0.442 | |
| 1ao8 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1q4u | 4CA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.441 | |
| 1sn5 | T3 | Transthyretin | / | 0.441 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.441 | |
| 3o15 | 3NM | Thiamine-phosphate synthase | / | 0.441 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 3uvp | 048 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 4ac0 | MIY | Tetracycline repressor protein class B from transposon Tn10 | / | 0.441 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.441 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4oty | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.441 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.441 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.441 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.440 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.440 | |
| 1kk4 | ACO | Streptogramin A acetyltransferase | 2.3.1 | 0.440 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.440 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.440 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.440 | |
| 2y3s | TIR | TamL | / | 0.440 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.440 | |
| 3zcw | 4A2 | Kinesin-like protein KIF11 | / | 0.440 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.440 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.440 | |
| 5c03 | AGS | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.440 |