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 |
|---|---|---|---|
| 3m34 | TPP | Transketolase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3m34 | TPP | Transketolase | / | 1.000 | |
| 3m7i | TPP | Transketolase | / | 0.650 | |
| 4c7x | TPP | Transketolase | / | 0.536 | |
| 3m6l | TPP | Transketolase | / | 0.535 | |
| 1wuu | ANP | Galactokinase | 2.7.1.6 | 0.490 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.489 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.478 | |
| 3r43 | ID8 | Aldo-keto reductase family 1 member C3 | / | 0.478 | |
| 2w02 | ATP | AcsD | / | 0.474 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.473 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.471 | |
| 5kj1 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.471 | |
| 4nmc | FAD | Bifunctional protein PutA | / | 0.468 | |
| 1evj | NAD | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.467 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.466 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.466 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.465 | |
| 3kr6 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.464 | |
| 5dby | NPS | Serum albumin | / | 0.463 | |
| 1jed | ADP | Sulfate adenylyltransferase | / | 0.462 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.462 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.462 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.461 | |
| 4guk | P2G | Neuronal calcium sensor 1 | / | 0.461 | |
| 1t90 | NAD | Malonate-semialdehyde dehydrogenase | 1.2.1.27 | 0.460 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.460 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.460 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.459 | |
| 1zji | 2PG | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.459 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.459 | |
| 2qiq | CYV | Replicase polyprotein 1ab | / | 0.459 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.458 | |
| 1h6b | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.458 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.458 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.458 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.458 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.458 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4iah | 1DX | Alr2278 protein | / | 0.458 | |
| 1asc | NPL | Aspartate aminotransferase | 2.6.1.1 | 0.457 | |
| 2bgl | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.457 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.457 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.457 | |
| 1dfo | PLG | Serine hydroxymethyltransferase | 2.1.2.1 | 0.456 | |
| 1t13 | INI | 6,7-dimethyl-8-ribityllumazine synthase 2 | / | 0.456 | |
| 2vcz | VC3 | Hematopoietic prostaglandin D synthase | / | 0.456 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.456 | |
| 3r4o | FU3 | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.455 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.454 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.454 | |
| 3i0a | DBH | Neutrophil gelatinase-associated lipocalin | / | 0.454 | |
| 3oq6 | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 5a8a | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.454 | |
| 1h6a | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.453 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.453 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.453 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.453 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.453 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.453 | |
| 1bpw | NAD | Betaine aldehyde dehydrogenase | 1.2.1.8 | 0.452 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.452 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.452 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.452 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.452 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 5kje | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2xpc | 051 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.451 | |
| 4ubt | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.451 | |
| 5dw5 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.451 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.450 | |
| 3ckq | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.450 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3gue | UPG | UTP-glucose-1-phosphate uridylyltransferase 2, putative | / | 0.450 | |
| 4xzj | NAD | Putative NAD(+)--arginine ADP-ribosyltransferase Vis | 2.4.2.31 | 0.450 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.449 | |
| 3srz | UPG | Toxin A | / | 0.449 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.449 | |
| 5dld | UD1 | UDP-N-Acetylglucosamine 2-epimerase | / | 0.449 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 3c1o | NAP | Eugenol synthase | / | 0.448 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4hai | I23 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.448 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.448 | |
| 1mez | GDP | Adenylosuccinate synthetase isozyme 1 | / | 0.447 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.447 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.447 | |
| 2oz0 | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.447 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.447 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.446 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.446 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.446 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.446 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.446 | |
| 3thr | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.446 | |
| 4e03 | ADP | Plasmid partitioning protein ParF | / | 0.446 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.445 | |
| 3frk | TQP | QdtB | / | 0.445 | |
| 3rbq | GLY_ALA_GLY_DAO | Protein unc-119 homolog A | / | 0.445 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 4g0k | 0VS | Glutathionyl-hydroquinone reductase YqjG | 1.8 | 0.445 | |
| 4m2b | UPG | UDP-glucose pyrophosphorylase | / | 0.445 | |
| 5c4n | NAP | Precorrin-6A reductase | 1.3.1.54 | 0.445 | |
| 1cjv | DAD | Adenylate cyclase type 2 | / | 0.444 | |
| 1cjv | DAD | Adenylate cyclase type 5 | / | 0.444 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.444 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2xvw | 9NR | Serum albumin | / | 0.444 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4oe4 | NAD | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial | 1.2.1.88 | 0.444 | |
| 4zgs | NAD | Putative D-lactate dehydrogenase | / | 0.444 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 2nli | FMN | Lactate oxidase | / | 0.443 | |
| 3e8x | NAP | BH1520 protein | / | 0.443 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3rr3 | FLR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.443 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.443 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.442 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.442 | |
| 2vqq | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.442 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.442 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4hjf | C2E | GGDEF family protein | / | 0.442 | |
| 4k36 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.442 | |
| 1nj6 | A5A | Proline--tRNA ligase | / | 0.441 | |
| 2uuo | LK3 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.441 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.441 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 3w1q | YRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.441 | |
| 4c6u | TLG | 3-oxoacyl-ACP synthase | / | 0.441 | |
| 4kiq | 1RA | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 4r2m | ANP | Universal stress protein F | / | 0.441 | |
| 4r3a | ANP | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.441 | |
| 4rgq | NDP | Glycerol-1-phosphate dehydrogenase [NAD(P)+] | / | 0.441 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1fml | RTL | Retinol dehydratase | / | 0.440 | |
| 1o02 | NAD | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.440 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 2oye | IM8 | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.440 | |
| 2wzm | NA7 | Uncharacterized oxidoreductase MSMEG_2407/MSMEI_2346 | / | 0.440 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 |