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 |
|---|---|---|---|
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 1.000 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.768 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.681 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.616 | |
| 2wya | HMG | Hydroxymethylglutaryl-CoA synthase, mitochondrial | 2.3.3.10 | 0.589 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.574 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.542 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.514 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.498 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.494 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.492 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.478 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.478 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.477 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.476 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.475 | |
| 1ysl | COA | Hydroxymethylglutaryl-CoA synthase | 2.3.3.10 | 0.474 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.474 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.473 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.472 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.470 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.470 | |
| 4nxx | GDP | Mitochondrial dynamics protein MID51 | / | 0.470 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.469 | |
| 2xvv | 9DN | Serum albumin | / | 0.469 | |
| 5dmh | ADP | 3-oxo-tetronate kinase | / | 0.469 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.468 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 4l8u | 9AZ | Serum albumin | / | 0.467 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.466 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.466 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.465 | |
| 2xvw | 9NR | Serum albumin | / | 0.464 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 2yee | 2EC | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 2e15 | SAH | Diphthine synthase | / | 0.459 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.459 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.458 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 3fun | 798 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.458 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.457 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.457 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.456 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.456 | |
| 2g78 | REA | Cellular retinoic acid-binding protein 2 | / | 0.456 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.456 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.456 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.456 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.455 | |
| 4u9a | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.455 | |
| 5dp2 | NAP | CurF | / | 0.455 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.454 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.453 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.452 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.452 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.452 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.452 | |
| 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 | 0.452 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.452 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.452 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.452 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.452 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.451 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.451 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.451 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.451 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.451 | |
| 1fml | RTL | Retinol dehydratase | / | 0.450 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.450 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 3b9l | AZZ | Serum albumin | / | 0.450 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.450 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3zxz | KRW | Hepatocyte growth factor receptor | 2.7.10.1 | 0.450 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.449 | |
| 2p6k | SAH | Diphthine synthase | / | 0.449 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.449 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.449 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.448 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.448 | |
| 2z6r | SAH | Diphthine synthase | / | 0.448 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.448 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.448 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.448 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.448 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.447 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.447 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.447 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.447 | |
| 2fa3 | ACO | Hydroxymethylglutaryl-CoA synthase | / | 0.447 | |
| 2p6l | SAH | Diphthine synthase | / | 0.447 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.447 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.447 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.447 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.446 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.446 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.446 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.446 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.445 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.445 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 2ejz | SAH | Diphthine synthase | / | 0.445 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.445 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.445 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1iy8 | NAD | Levodione reductase | / | 0.444 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.444 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.444 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.444 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.443 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 1qf4 | RPD | Adenylosuccinate synthetase | / | 0.443 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2egl | SAH | Diphthine synthase | / | 0.443 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.443 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.443 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.443 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.443 | |
| 3ful | 52D | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.443 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.443 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.443 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.442 | |
| 1uy9 | PU6 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.442 | |
| 2bxq | IMN | Serum albumin | / | 0.442 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.442 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.442 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.442 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.442 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.442 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.442 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.441 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.441 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.441 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.441 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.441 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.441 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.441 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.440 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.440 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.440 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2gqp | PA7 | Endoplasmin | / | 0.440 | |
| 2pca | SAH | Diphthine synthase | / | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3fuh | BES | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.440 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.440 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3nbv | ANP | Ketohexokinase | / | 0.440 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.440 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.440 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.440 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.440 |