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 |
|---|---|---|---|
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 1.000 | |
| 2gtb | AZP | Orf1ab polyprotein | / | 0.621 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.505 | |
| 2qiq | CYV | Replicase polyprotein 1ab | / | 0.505 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.491 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.489 | |
| 2gz8 | F3F | Orf1a polyprotein | / | 0.489 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.484 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.481 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.480 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.476 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.473 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.473 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.470 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.466 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.466 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.466 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.465 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.465 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.460 | |
| 2op9 | WR1 | Orf1ab polyprotein | / | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.459 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.459 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.459 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.458 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.458 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.458 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.458 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.458 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.458 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.457 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.456 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.456 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.456 | |
| 4yqf | GDP | Septin-9 | / | 0.456 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.455 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.454 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.454 | |
| 5dw5 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.454 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.453 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.453 | |
| 3a3g | DLZ | Lumazine protein | / | 0.451 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.451 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.450 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.450 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.450 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.450 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.450 | |
| 4gm4 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.450 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.450 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.450 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.449 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.449 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.449 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.448 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.448 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.448 | |
| 4mpr | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.448 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.447 | |
| 3q5l | KX2 | Heat shock protein 83-1 | / | 0.446 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.446 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.446 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.446 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.445 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.445 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.445 | |
| 1l2t | ATP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.444 | |
| 1po7 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.444 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.444 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.444 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.444 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.442 | |
| 2egl | SAH | Diphthine synthase | / | 0.442 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.442 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.442 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2egs | SAH | Diphthine synthase | / | 0.441 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.441 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.441 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.440 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 5a9s | NAP | Putative dehydrogenase | / | 0.440 |