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 |
|---|---|---|---|
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 1.000 | |
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.658 | |
| 3pd5 | TSB | Threonine--tRNA ligase | 6.1.1.3 | 0.620 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.597 | |
| 3pd2 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.594 | |
| 3pd3 | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.573 | |
| 4rrf | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.569 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.564 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.563 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.545 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.539 | |
| 4rrm | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.526 | |
| 4rrh | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.525 | |
| 4rra | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.513 | |
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.513 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.496 | |
| 4rrb | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.492 | |
| 4rr8 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.487 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.484 | |
| 4rrd | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.483 | |
| 4rrl | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.483 | |
| 4rrc | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.481 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.474 | |
| 5cvh | ADP | Casein kinase II subunit alpha | 2.7.11.1 | 0.471 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.470 | |
| 4i9i | 1DY | Tankyrase-1 | 2.4.2.30 | 0.469 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.469 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.468 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1r2j | FAD | FkbI | / | 0.467 | |
| 1syn | F89 | Thymidylate synthase | / | 0.467 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.467 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.467 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.466 | |
| 1q4x | G24 | Thyroid hormone receptor beta | / | 0.465 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.465 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.465 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.465 | |
| 4bgg | 844 | Activin receptor type-1 | 2.7.11.30 | 0.464 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4rrk | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.462 | |
| 1od1 | 0QS | Endothiapepsin | 3.4.23.22 | 0.461 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2acw | UPG | Glycosyltransferase | / | 0.459 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.459 | |
| 1fml | RTL | Retinol dehydratase | / | 0.458 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.458 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.458 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 4bfp | SWY | Tankyrase-2 | 2.4.2.30 | 0.457 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.456 | |
| 3pgi | F41 | Endothiapepsin | 3.4.23.22 | 0.456 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.456 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3mtf | A3F | Activin receptor type-1 | 2.7.11.30 | 0.455 | |
| 3v49 | PK0 | Androgen receptor | / | 0.454 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.454 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.454 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.453 | |
| 4rr9 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.453 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.452 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.452 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.452 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.451 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.451 | |
| 4fa6 | 0TA | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.451 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.451 | |
| 4oac | ADP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.450 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.450 | |
| 5k0s | 0OU | Methionine--tRNA ligase | / | 0.450 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.449 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.449 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.449 | |
| 3nhw | ZXZ | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.449 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.449 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1q4u | 4CA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.448 | |
| 1rb2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.448 | |
| 4c4h | 7RO | Dual specificity protein kinase TTK | 2.7.12.1 | 0.448 | |
| 4rrx | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.448 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.448 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.447 | |
| 4gu6 | 10N | Focal adhesion kinase 1 | 2.7.10.2 | 0.447 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.446 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.446 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.446 | |
| 2xik | J60 | Serine/threonine-protein kinase 25 | 2.7.11.1 | 0.446 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.446 | |
| 4m48 | 21B | Sodium-dependent dopamine transporter | / | 0.446 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.445 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.445 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.445 | |
| 2rg6 | 287 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3q5k | D1U | Heat shock protein 83-1 | / | 0.445 | |
| 3u9n | 09H | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.445 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.445 | |
| 4li6 | 1XO | Tankyrase-1 | 2.4.2.30 | 0.445 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.445 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.445 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.444 | |
| 1qiw | DPD | Calmodulin | / | 0.444 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.444 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.444 | |
| 2r8p | T6F | Transketolase 1 | / | 0.444 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.444 | |
| 4lm5 | Q17 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.444 | |
| 4zea | IMI | Endothiapepsin | 3.4.23.22 | 0.444 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.444 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.443 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.443 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 2xiz | XIZ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.443 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.443 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.443 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.443 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2fum | MIX | Serine/threonine-protein kinase PknB | 2.7.11.1 | 0.442 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.442 | |
| 2r8o | T5X | Transketolase 1 | / | 0.442 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.442 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.442 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.442 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 1qkn | RAL | Estrogen receptor beta | / | 0.441 | |
| 1z95 | 198 | Androgen receptor | / | 0.441 | |
| 2cd8 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.441 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2jjj | 0QS | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3q9w | EMO | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.440 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.440 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1u54 | ACP | Activated CDC42 kinase 1 | / | 0.440 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.440 | |
| 2wgj | VGH | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.440 | |
| 3uxh | UXH | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4bch | T7Z | Cyclin-dependent kinase 9 | 2.7.11.22 | 0.440 | |
| 4bzo | 676 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.440 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.440 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.440 | |
| 4y57 | F63 | Endothiapepsin | 3.4.23.22 | 0.440 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.440 |