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 |
|---|---|---|---|
| 4rrb | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4rrb | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 1.000 | |
| 4rrh | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.726 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.725 | |
| 4rrm | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.689 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.663 | |
| 4rra | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.653 | |
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.622 | |
| 4rr8 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.611 | |
| 4rr9 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.611 | |
| 4rrc | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.611 | |
| 4rrd | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.608 | |
| 4rrl | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.605 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.559 | |
| 4rrj | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.556 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.552 | |
| 4rrk | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.547 | |
| 3pd2 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.540 | |
| 3pd3 | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.533 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.528 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.525 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.513 | |
| 4rrf | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.512 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.504 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.500 | |
| 3pd5 | TSB | Threonine--tRNA ligase | 6.1.1.3 | 0.497 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.496 | |
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.487 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.480 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.480 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.478 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.477 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.475 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.473 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.473 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.472 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.471 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.468 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.467 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.467 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.466 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.465 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.465 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.464 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.464 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.464 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.463 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.458 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.458 | |
| 1r2j | FAD | FkbI | / | 0.457 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.457 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.456 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.456 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.456 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.455 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.454 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.454 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.454 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4kc4 | WS3 | Histo-blood group ABO system transferase | / | 0.453 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.452 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.452 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3frk | TQP | QdtB | / | 0.452 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.452 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.451 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.451 | |
| 3ix3 | OHN | Transcriptional activator protein LasR | / | 0.451 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.451 | |
| 4kc1 | WS1 | Histo-blood group ABO system transferase | / | 0.451 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.450 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.450 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.450 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.450 | |
| 1ddt | APU | Diphtheria toxin | / | 0.449 | |
| 1q4x | G24 | Thyroid hormone receptor beta | / | 0.449 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.449 | |
| 2zul | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.449 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.449 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.449 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.449 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 2bgj | FAD | NADPH:ferredoxin reductase | / | 0.448 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.448 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 3p0g | P0G | Beta-2 adrenergic receptor | / | 0.448 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1rq1 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.447 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.447 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.447 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.447 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.447 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.447 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.446 | |
| 1ppl | 1Z7 | Penicillopepsin-1 | 3.4.23.20 | 0.446 | |
| 3dya | PZL | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.446 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.446 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.445 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.445 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.445 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.445 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.445 | |
| 4qbj | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.445 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.445 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 1bux | PPS | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.444 | |
| 1eyy | NAP | NADP-dependent fatty aldehyde dehydrogenase | 1.2.1.4 | 0.444 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.444 | |
| 1xp8 | AGS | Protein RecA | / | 0.444 | |
| 1zdw | FLV | Prenyltransferase | / | 0.444 | |
| 2vqo | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.444 | |
| 2vqq | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.444 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.444 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.444 | |
| 3n1s | 5GP | Purine nucleoside phosphoramidase | / | 0.444 | |
| 4b8z | GDP | GDP-L-fucose synthase | 1.1.1.271 | 0.444 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.444 | |
| 4e2b | FMN | Dehydrogenase | / | 0.444 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.444 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 1n3r | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.443 | |
| 1q3a | NGH | Stromelysin-2 | 3.4.24.22 | 0.443 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.443 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 3t0k | DCQ | Sulfide-quinone reductase | / | 0.443 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.443 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.443 | |
| 4z9g | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.443 | |
| 1pw1 | HEL | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.442 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.442 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.442 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.442 | |
| 2wp9 | CBE | Succinate dehydrogenase iron-sulfur subunit | 1.3.5.1 | 0.442 | |
| 2wp9 | CBE | Succinate dehydrogenase cytochrome b556 subunit | / | 0.442 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3lnb | COA | N-acetyltransferase family protein | / | 0.442 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.442 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.442 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.442 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.441 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.441 | |
| 2bpo | FAD | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.441 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.441 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.441 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.441 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.441 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.441 | |
| 4ejn | 0R4 | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.441 | |
| 4lde | P0G | Beta-2 adrenergic receptor | / | 0.441 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.440 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.440 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.440 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.440 | |
| 3zy5 | GFB | GDP-fucose protein O-fucosyltransferase 1 | 2.4.1.221 | 0.440 | |
| 4bl5 | GFB | GDP-L-fucose synthase | 1.1.1.271 | 0.440 | |
| 4l4x | NDP | AmphI | / | 0.440 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.440 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.440 |