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 |
|---|---|---|---|
| 1z5v | GSP | Tubulin gamma-1 chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1z5v | GSP | Tubulin gamma-1 chain | / | 1.000 | |
| 1z5w | GTP | Tubulin gamma-1 chain | / | 0.730 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.528 | |
| 4wbn | GTP | Tubulin alpha-1B chain | / | 0.513 | |
| 4ihj | GTP | Tubulin alpha-1B chain | / | 0.500 | |
| 4o4l | GTP | Tubulin alpha-1B chain | / | 0.493 | |
| 4tv9 | GTP | Tubulin alpha-1B chain | / | 0.486 | |
| 4zol | GTP | Tubulin alpha-1B chain | / | 0.483 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.480 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.474 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.474 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.473 | |
| 5jqg | GTP | Tubulin alpha-1B chain | / | 0.473 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.472 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.471 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.470 | |
| 4tuy | GTP | Tubulin alpha-1B chain | / | 0.470 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.469 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.465 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.465 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.465 | |
| 1ri1 | GTG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.463 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.463 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.463 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.462 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.462 | |
| 4iij | GTP | Tubulin alpha-1B chain | / | 0.461 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.460 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.460 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.460 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.459 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4f6r | GDP | Tubulin beta chain | / | 0.459 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.458 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.458 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.458 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.456 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.456 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4gt8 | ADP | Sensor protein VraS | 2.7.13.3 | 0.456 | |
| 4qfy | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.456 | |
| 5la6 | GTP | Tubulin alpha-1B chain | / | 0.456 | |
| 3vmm | P0D | Alanine--anticapsin ligase | / | 0.455 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.454 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.454 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.454 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.454 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.454 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.453 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.453 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.453 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.452 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.450 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.450 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.450 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.450 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.450 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.449 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.449 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.449 | |
| 2vhq | ATP | NTPase P4 | / | 0.449 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.449 | |
| 3swq | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.449 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.449 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.448 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.448 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.448 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 6gsu | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.448 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.447 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.447 | |
| 1xag | NAD | 3-dehydroquinate synthase | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 5dp2 | NAP | CurF | / | 0.447 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.446 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.446 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
| 4o4i | GTP | Tubulin alpha-1B chain | / | 0.446 | |
| 5doz | NDP | JamJ | / | 0.446 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.446 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.445 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.445 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.445 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.445 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.445 | |
| 5bn3 | ADP | V-type ATP synthase alpha chain | / | 0.445 | |
| 5bn3 | ADP | NEQ263 | / | 0.445 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.444 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.444 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.444 | |
| 4gn6 | TYL | Lactoperoxidase | 1.11.1.7 | 0.444 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.443 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.443 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.443 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.443 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.443 | |
| 4yer | ADP | Antibiotic ABC transporter, ATP-binding protein, putative | / | 0.443 | |
| 1i91 | INQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.442 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 3ryh | GTP | Tubulin alpha chain | / | 0.442 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.442 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.442 | |
| 1cbf | SAH | Cobalt-precorrin-4 C(11)-methyltransferase | 2.1.1.271 | 0.441 | |
| 1p0h | COA | Mycothiol acetyltransferase | 2.3.1.189 | 0.441 | |
| 1p3d | UMA | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.441 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.441 | |
| 2nr4 | FMN | Conserved protein | / | 0.441 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.440 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 4l5a | TBN | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 4pzr | COA | Histone acetyltransferase p300 | / | 0.440 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.440 |