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 |
|---|---|---|---|
| 3oe1 | TDL | Pyruvate decarboxylase | 4.1.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3oe1 | TDL | Pyruvate decarboxylase | 4.1.1.1 | 1.000 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.621 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.531 | |
| 1ovm | TPP | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.529 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.512 | |
| 4cok | TPP | Pyruvate decarboxylase | / | 0.509 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.497 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.491 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.474 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.473 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.473 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.473 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.467 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.466 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.464 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.463 | |
| 2w93 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.462 | |
| 1uyh | PU0 | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.460 | |
| 2y5s | 78H | Dihydropteroate synthase | / | 0.459 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.459 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.459 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.458 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.457 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.456 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.455 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.455 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.454 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.454 | |
| 1qpb | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.453 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.452 | |
| 2p2x | SAH | Diphthine synthase | / | 0.451 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.451 | |
| 4m0l | GDP | Translation initiation factor 2 subunit gamma | / | 0.451 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.450 | |
| 2vk4 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.450 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.449 | |
| 2wet | FAD | Tryptophan 5-halogenase | / | 0.449 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.449 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.448 | |
| 1c6y | MK1 | Protease | / | 0.447 | |
| 2q5o | PPY | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.447 | |
| 4iwq | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.447 | |
| 5ify | UMP | Glucose-1-phosphate thymidylyltransferase | / | 0.447 | |
| 1g67 | TZP | Thiamine-phosphate synthase | / | 0.446 | |
| 2c47 | 5ID | Casein kinase I isoform gamma-2 | / | 0.446 | |
| 2jfg | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.446 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.446 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4b1i | A8P | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.445 | |
| 4dx7 | DM2 | Multidrug efflux pump subunit AcrB | / | 0.445 | |
| 4hjf | C2E | GGDEF family protein | / | 0.445 | |
| 3ld6 | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.444 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.444 | |
| 4i9b | NAD | Putative betaine aldehyde dehyrogenase | / | 0.444 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.443 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2pwc | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.443 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.442 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.442 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.442 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.442 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.442 | |
| 4d86 | ADP | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.442 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.442 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.442 | |
| 1bv9 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.441 | |
| 3liv | E16 | Protease | / | 0.441 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.441 | |
| 4j54 | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4nfs | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 4qq3 | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.441 | |
| 4e32 | DWN | Methyltransferase | / | 0.440 |