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 |
|---|---|---|---|
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 1.000 | |
| 1upa | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.849 | |
| 1upb | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.829 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.725 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.608 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.599 | |
| 2q5o | PPY | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.539 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.525 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.514 | |
| 2c3y | HTL | Pyruvate synthase | / | 0.484 | |
| 2c3o | TPP | Pyruvate synthase | / | 0.481 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.481 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.478 | |
| 2uza | HTL | Pyruvate synthase | / | 0.478 | |
| 2pan | TDP | Glyoxylate carboligase | 4.1.1.47 | 0.475 | |
| 2pda | TPP | Pyruvate synthase | / | 0.472 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.471 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.470 | |
| 4fgh | 0U6 | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4zth | GG5 | Mitogen-activated protein kinase 14 | / | 0.468 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.466 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.464 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.463 | |
| 1j7k | ATP | Holliday junction ATP-dependent DNA helicase RuvB | / | 0.462 | |
| 4eh3 | IRG | Mitogen-activated protein kinase 14 | / | 0.462 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.462 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.461 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.461 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.461 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.460 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.460 | |
| 1kek | HTL | Pyruvate synthase | / | 0.459 | |
| 2c3p | 1TP | Pyruvate synthase | / | 0.459 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.459 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.459 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.458 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.457 | |
| 2i0y | 5CN | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.457 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.457 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.456 | |
| 1uyk | PUX | Heat shock protein HSP 90-alpha | / | 0.456 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.456 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.456 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.456 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.456 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.455 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.455 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.455 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.455 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.454 | |
| 4yt5 | H4M | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | / | 0.454 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.453 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.453 | |
| 2fwy | H64 | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.452 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.452 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 4g8b | HL6 | Alpha/beta hydrolase fold protein | / | 0.451 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.450 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.450 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.450 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.450 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.449 | |
| 2c3u | 2TP | Pyruvate synthase | / | 0.449 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.449 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.449 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.449 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.449 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.448 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.448 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.447 | |
| 3exn | ACO | Probable acetyltransferase | / | 0.447 | |
| 4j0s | 1H3 | Bromodomain-containing protein 4 | / | 0.447 | |
| 1syn | F89 | Thymidylate synthase | / | 0.446 | |
| 1w78 | PD8 | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.446 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.446 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.446 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.446 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3tij | URI | Nucleoside permease | / | 0.446 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.446 | |
| 4aa4 | QC0 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.446 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.446 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 2xhx | T5M | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.445 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.445 | |
| 3ih0 | ANP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.445 | |
| 4asy | N5Y | Glucose-1-phosphate thymidylyltransferase | / | 0.445 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.445 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 1ke7 | LS3 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.444 | |
| 1vj3 | TAB | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.444 | |
| 2wxv | WXV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.443 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.443 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.443 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3oom | 507 | Activin receptor type-1 | 2.7.11.30 | 0.443 | |
| 3rfx | NAD | Uronate dehydrogenase | / | 0.443 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1g9c | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.442 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.442 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.442 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.442 | |
| 3hz1 | 37D | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.442 | |
| 4c9o | CAM | Cytochrome P450 | / | 0.442 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.442 | |
| 4iwv | 1J9 | Glucokinase | 2.7.1.2 | 0.442 | |
| 4qzs | JQ1 | Bromodomain-containing protein 4 | / | 0.442 | |
| 1jsc | TPP | Acetolactate synthase catalytic subunit, mitochondrial | 2.2.1.6 | 0.441 | |
| 1nqm | BTN | Streptavidin | / | 0.441 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2fzi | DH3 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2pvj | P44 | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 3l3r | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.441 | |
| 4h4e | 10G | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | / | 0.441 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3hhu | 819 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 | |
| 4ixg | IXG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.440 | |
| 4nh8 | 2LC | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.440 |