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 |
|---|---|---|---|
| 1xvv | CCQ | L-carnitine CoA-transferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1xvv | CCQ | L-carnitine CoA-transferase | / | 1.000 | |
| 1xa4 | COA | L-carnitine CoA-transferase | / | 0.553 | |
| 1xvt | COA | L-carnitine CoA-transferase | / | 0.535 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.493 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.491 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.489 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.488 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.485 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.481 | |
| 1yci | NDF | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.477 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.477 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.477 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.476 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.474 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.471 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.470 | |
| 3eku | CY9 | Actin-5C | / | 0.470 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.469 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.467 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.467 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.466 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.465 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.465 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.464 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.463 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2zse | ACP | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.462 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.461 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.461 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.461 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.461 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.460 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.459 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.458 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.457 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.457 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.457 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.457 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.457 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.456 | |
| 4clo | NAP | Pteridine reductase | / | 0.456 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.456 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.455 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.454 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 1v2h | GUN | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 2dxi | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.454 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.454 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.454 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.454 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.453 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.453 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.451 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.450 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.450 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.450 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.450 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.450 | |
| 1v45 | 3DG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.449 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 3e4a | QIX | Insulin-degrading enzyme | 3.4.24.56 | 0.448 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.448 | |
| 1hzz | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.447 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.447 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.446 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.446 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.446 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.445 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.445 | |
| 1sg0 | STL | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.445 | |
| 2wp9 | CBE | Succinate dehydrogenase iron-sulfur subunit | 1.3.5.1 | 0.445 | |
| 2wp9 | CBE | Succinate dehydrogenase cytochrome b556 subunit | / | 0.445 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.445 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.445 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.445 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.444 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2g0b | NLT | Long-chain N-acyl amino acid synthase | / | 0.444 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.444 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.444 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.444 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.444 | |
| 4wbd | ADP | Putative cysteine ligase BshC | / | 0.444 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.443 | |
| 5bqf | NAP | Probable hydroxyacid dehydrogenase protein | / | 0.443 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.442 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.442 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.442 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.441 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.441 | |
| 1wm1 | PTB | Proline iminopeptidase | 3.4.11.5 | 0.441 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.441 | |
| 1x2b | STX | Proline iminopeptidase | 3.4.11.5 | 0.441 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.441 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.441 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.441 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.441 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.440 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.440 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.440 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.440 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.440 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.440 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.440 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.440 |