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 |
|---|---|---|---|
| 1z5v | GSP | Tubulin gamma-1 chain |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1z5v | GSP | Tubulin gamma-1 chain | / | 1.000 | |
| 1z5w | GTP | Tubulin gamma-1 chain | / | 0.730 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.526 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.485 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.484 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.480 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.475 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.472 | |
| 3g11 | P9C | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.472 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.470 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.469 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.467 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.465 | |
| 4b45 | GSP | Tubulin-like protein CetZ2 | / | 0.465 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.464 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.463 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.463 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.462 | |
| 1ri1 | GTG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.462 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.461 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.459 | |
| 1tys | TMP | Thymidylate synthase | / | 0.458 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.458 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.458 | |
| 4f6r | GDP | Tubulin beta chain | / | 0.458 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.456 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.456 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.456 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.456 | |
| 4gt8 | ADP | Sensor protein VraS | 2.7.13.3 | 0.456 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.455 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.455 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.454 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.454 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.454 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.454 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.454 | |
| 1w19 | T5P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.453 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.453 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.452 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.452 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.450 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.449 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.449 | |
| 4z87 | 5GP | Inosine-5'-monophosphate dehydrogenase | / | 0.449 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.449 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.447 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.447 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.446 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.446 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.446 | |
| 3ho9 | N3A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.446 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.446 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.445 | |
| 4qfy | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.445 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.444 | |
| 2gz7 | D3F | Orf1a polyprotein | / | 0.444 | |
| 6gsu | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.444 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.443 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.443 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.443 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.443 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.443 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.443 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.443 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.443 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.443 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.443 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.443 | |
| 5dp2 | NAP | CurF | / | 0.443 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1i91 | INQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.442 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.442 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.442 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.442 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.441 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.441 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.441 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2wp9 | CBE | Succinate dehydrogenase iron-sulfur subunit | 1.3.5.1 | 0.441 | |
| 2wp9 | CBE | Succinate dehydrogenase cytochrome b556 subunit | / | 0.441 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.441 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.441 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 4uxq | 0LI | Fibroblast growth factor receptor 4 | 2.7.10.1 | 0.441 | |
| 1z3c | SA8 | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.440 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.440 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.440 |