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 |
|---|---|---|---|
| 2uz1 | TPP | Benzaldehyde lyase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2uz1 | TPP | Benzaldehyde lyase | / | 1.000 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.600 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.556 | |
| 3iaf | TPP | Benzaldehyde lyase | / | 0.536 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.522 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.517 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.501 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.498 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.495 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.486 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.484 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.483 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.482 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.481 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.481 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.474 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.473 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.473 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.471 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 2ji6 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.470 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.468 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.468 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.466 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.466 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.465 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.465 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.465 | |
| 4em9 | TCE | Peroxisome proliferator-activated receptor gamma | / | 0.463 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.462 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.461 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.461 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.460 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.457 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.457 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.457 | |
| 3say | OFT | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.457 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.456 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.455 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.455 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.454 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.454 | |
| 4juc | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.454 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.453 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.453 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.453 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.452 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.452 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.452 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.452 | |
| 3e8r | 615 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.452 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.452 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.452 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.451 | |
| 2zgy | GDP | Plasmid segregation protein ParM | / | 0.451 | |
| 3cz7 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.451 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.451 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.451 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.450 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.450 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 2fwz | H71 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.450 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.449 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.449 | |
| 2ejz | SAH | Diphthine synthase | / | 0.449 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.449 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.448 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.448 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.448 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.447 | |
| 4awp | 99A | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.447 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.447 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.446 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.446 | |
| 2uzf | CAA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.446 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.446 | |
| 3d8b | ADP | Fidgetin-like protein 1 | 3.6.4 | 0.446 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.446 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4xul | GTP | Uncharacterized protein mg662 | / | 0.446 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.446 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.446 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.445 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.445 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.445 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.445 | |
| 4u7w | NDP | MxaA | / | 0.445 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.445 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3rnn | RNN | Glutamate receptor 2 | / | 0.444 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.444 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.444 | |
| 4qgi | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.444 | |
| 4v12 | POG | MaoC like domain protein | / | 0.444 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.444 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2fav | APR | Nonstructural polyprotein pp1a | / | 0.443 | |
| 2g0g | SP0 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.443 | |
| 3hwx | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.443 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.443 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.443 | |
| 5ej8 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.443 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.442 | |
| 1q19 | SSC | Carbapenam-3-carboxylate synthase | 6.3.3.6 | 0.442 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.442 | |
| 2c31 | TZD | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.442 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.442 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.442 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.442 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.442 | |
| 5ej6 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.442 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.441 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.441 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.441 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.441 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.441 | |
| 1ezv | UQ6 | Cytochrome b | / | 0.440 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3r32 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.440 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.440 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.440 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.440 |