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 |
|---|---|---|---|
| 4rrb | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity 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 | 0.558 | |
| 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 | 0.524 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.512 | |
| 4rrf | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.512 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.506 | |
| 3pd5 | TSB | Threonine--tRNA ligase | 6.1.1.3 | 0.503 | |
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.487 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.480 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.479 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.478 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.475 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.473 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.471 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.471 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.470 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.470 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.469 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.466 | |
| 1fml | RTL | Retinol dehydratase | / | 0.465 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.464 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.464 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.463 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.463 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.461 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.461 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.460 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.460 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.458 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.457 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4kc4 | WS3 | Histo-blood group ABO system transferase | / | 0.457 | |
| 4xz3 | COA | Acyl-CoA synthetase (NDP forming) | / | 0.457 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.457 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.456 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.456 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.456 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.456 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.456 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.455 | |
| 3cx4 | ADP | Glycogen synthase | 2.4.1.21 | 0.455 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.455 | |
| 4kc1 | WS1 | Histo-blood group ABO system transferase | / | 0.455 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.454 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.454 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.454 | |
| 4awp | 99A | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.454 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.453 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.453 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.453 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.452 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.452 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.452 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.451 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.451 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.450 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.450 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.450 | |
| 4g2i | 0VQ | Vitamin D3 receptor | / | 0.450 | |
| 1q4x | G24 | Thyroid hormone receptor beta | / | 0.449 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.449 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.449 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.449 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.448 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.448 | |
| 2xvw | 9NR | Serum albumin | / | 0.448 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 1ddt | APU | Diphtheria toxin | / | 0.447 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 1rq1 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.447 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.447 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.447 | |
| 3ix3 | OHN | Transcriptional activator protein LasR | / | 0.447 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.447 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.447 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.447 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.447 | |
| 1ppl | 1Z7 | Penicillopepsin-1 | 3.4.23.20 | 0.446 | |
| 1r2j | FAD | FkbI | / | 0.446 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.446 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.446 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.446 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.446 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.446 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.446 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.445 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.445 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.445 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.445 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.445 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.445 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.445 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.445 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.445 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.444 | |
| 1eyy | NAP | NADP-dependent fatty aldehyde dehydrogenase | 1.2.1.4 | 0.444 | |
| 1if7 | SBR | Carbonic anhydrase 2 | 4.2.1.1 | 0.444 | |
| 1xp8 | AGS | Protein RecA | / | 0.444 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.444 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.444 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.444 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4e2d | FMN | Dehydrogenase | / | 0.444 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.443 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.443 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.443 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.443 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 2r4u | ADP | Glycogen synthase | 2.4.1.21 | 0.443 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.443 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.443 | |
| 3t0k | DCQ | Sulfide-quinone reductase | / | 0.443 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.443 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.442 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.442 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.442 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.442 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.442 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.441 | |
| 1pw1 | HEL | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.441 | |
| 1zdw | FLV | Prenyltransferase | / | 0.441 | |
| 3dya | PZL | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.441 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.441 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.441 | |
| 2bxq | IMN | Serum albumin | / | 0.440 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.440 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.440 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.440 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.440 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.440 | |
| 3nga | 3NG | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 3sfh | 1DI | Histone deacetylase 8 | 3.5.1.98 | 0.440 | |
| 3zy5 | GFB | GDP-fucose protein O-fucosyltransferase 1 | 2.4.1.221 | 0.440 | |
| 4b8z | GDP | GDP-L-fucose synthase | 1.1.1.271 | 0.440 | |
| 4bl5 | GFB | GDP-L-fucose synthase | 1.1.1.271 | 0.440 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 5jad | FB2 | Platelet-activating factor acetylhydrolase | 3.1.1.47 | 0.440 |