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 |
|---|---|---|---|
| 2j5s | KTA | Alr4455 protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2j5s | KTA | Alr4455 protein | / | 1.000 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.489 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.487 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.478 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.476 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.474 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.471 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.470 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.470 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.469 | |
| 1zdw | FLV | Prenyltransferase | / | 0.468 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.468 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.466 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.466 | |
| 3ar4 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.465 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.465 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.465 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 3ukr | CKH | Actin-related protein 3 | / | 0.464 | |
| 3ukr | CKH | Actin-related protein 2 | / | 0.464 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.464 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.464 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.463 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.463 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.463 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.463 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.462 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.460 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.458 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.458 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.458 | |
| 3wsb | RWZ | Farnesyltransferase, putative | / | 0.458 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.457 | |
| 3w8z | HTK | Putative FAD-dependent oxygenase EncM | / | 0.457 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 4c1i | EH9 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.457 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.457 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.456 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.456 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.456 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.456 | |
| 3zw3 | ZW3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.456 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.455 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.455 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.455 | |
| 1err | RAL | Estrogen receptor | / | 0.454 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.454 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.454 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.454 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1dgg | NDP | Catalase | 1.11.1.6 | 0.453 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.453 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 5dhg | DGV | Nociceptin receptor | / | 0.453 | |
| 3v49 | PK0 | Androgen receptor | / | 0.452 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.452 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.451 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.451 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.450 | |
| 2gs7 | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.450 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.450 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.449 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.449 | |
| 3wix | LC3 | Induced myeloid leukemia cell differentiation protein Mcl-1 | / | 0.449 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.449 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 3up0 | D7S | aceDAF-12 | / | 0.448 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.447 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.447 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.447 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.447 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.446 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.446 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.446 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.446 | |
| 4qe6 | JN3 | Bile acid receptor | / | 0.446 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1e8x | ATP | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.445 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.445 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.445 | |
| 3sw7 | 19K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.445 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.445 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.444 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.444 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3lm9 | ADP | Putative fructokinase | 2.7.1.4 | 0.444 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.444 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 1ao8 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.443 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1bux | PPS | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.442 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.442 | |
| 3ar6 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.442 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.442 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.442 | |
| 4fm5 | DF0 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.442 | |
| 4hxy | NDP | Plm1 | / | 0.442 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4m10 | ICD | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.442 | |
| 1ddt | APU | Diphtheria toxin | / | 0.441 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.441 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.441 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.441 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.440 | |
| 3oev | 3OE | Proteasome subunit beta type-5 | 3.4.25.1 | 0.440 | |
| 3oev | 3OE | Proteasome subunit beta type-6 | 3.4.25.1 | 0.440 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.440 | |
| 3tqa | NDP | Dihydrofolate reductase | / | 0.440 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.440 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.440 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.440 | |
| 4xz3 | COA | Acyl-CoA synthetase (NDP forming) | / | 0.440 | |
| 5jad | FB2 | Platelet-activating factor acetylhydrolase | 3.1.1.47 | 0.440 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.440 |