sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3r34 | COA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3r34 | COA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 1.000 | |
| 3r37 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.657 | |
| 3r3f | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.642 | |
| 3r3d | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.626 | |
| 3r3c | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.618 | |
| 3tea | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.610 | |
| 3r32 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.606 | |
| 3r3b | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.602 | |
| 3r35 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.594 | |
| 1q4u | 4CA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.581 | |
| 1q4t | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.569 | |
| 1wlv | COA | Phenylacetic acid degradation protein PaaI | / | 0.513 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.469 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.465 | |
| 4gah | 0ET | Acyl-coenzyme A thioesterase THEM4 | 3.1.2.2 | 0.465 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.464 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.464 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.459 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.459 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.457 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.456 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.455 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.455 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.454 | |
| 5a3c | NAD | SIR2 family protein | / | 0.454 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.453 | |
| 3u4u | LNH | Casein kinase II subunit alpha | 2.7.11.1 | 0.453 | |
| 4bzn | UGX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.453 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 5c41 | ACP | Ribokinase | / | 0.451 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.450 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.450 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.450 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.450 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.449 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.449 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.449 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.449 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.448 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.448 | |
| 5a3b | APR | SIR2 family protein | / | 0.448 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.447 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.447 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.446 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.446 | |
| 1tqp | ATP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.445 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.445 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.444 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.444 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.443 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.443 | |
| 3nwz | COA | BH2602 protein | / | 0.442 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.442 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.441 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.441 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 4l9k | EHF | Serum albumin | / | 0.441 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.440 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.440 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.440 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 |