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 |
|---|---|---|---|
| 3g0b | T22 | Dipeptidyl peptidase 4 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3g0b | T22 | Dipeptidyl peptidase 4 | / | 1.000 | |
| 3g0d | XIH | Dipeptidyl peptidase 4 | / | 0.712 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.704 | |
| 3ccc | 7AC | Dipeptidyl peptidase 4 | / | 0.656 | |
| 3opm | LUI | Dipeptidyl peptidase 4 | / | 0.628 | |
| 4g1f | 0WG | Dipeptidyl peptidase 4 | / | 0.583 | |
| 3qbj | NXZ | Dipeptidyl peptidase 4 | / | 0.537 | |
| 2aj8 | SC3 | Dipeptidyl peptidase 4 | / | 0.515 | |
| 3f8s | PF2 | Dipeptidyl peptidase 4 | / | 0.505 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.497 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.494 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.492 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.490 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 4ffw | 715 | Dipeptidyl peptidase 4 | / | 0.482 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.480 | |
| 4lut | DCS | Alanine racemase | / | 0.479 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.478 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.478 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.474 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.473 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.472 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.471 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.466 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.465 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.465 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.464 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.464 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.463 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.461 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.461 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.461 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.461 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.461 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.460 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.459 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.459 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.458 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.458 | |
| 3hf3 | FMN | Chromate reductase | / | 0.458 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.458 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.457 | |
| 1o1s | 1NH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.456 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.456 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.456 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.456 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.455 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.455 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.455 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.454 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2rgu | 356 | Dipeptidyl peptidase 4 | / | 0.453 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.453 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.453 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.453 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.453 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.452 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.451 | |
| 2wvm | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.451 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.451 | |
| 3ukf | GDU | UDP-galactopyranose mutase | / | 0.451 | |
| 1p4a | PCP | Pur operon repressor | / | 0.450 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.450 | |
| 4e2y | JHZ | Methyltransferase | / | 0.450 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.450 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.449 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.448 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.448 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.448 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.448 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.448 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.448 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.448 | |
| 1r6t | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.447 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.447 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.447 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.447 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.447 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.447 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.446 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.446 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3af4 | GCP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.446 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.446 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.446 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.445 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.445 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.445 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.445 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.445 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.444 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.444 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.444 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.444 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.444 | |
| 3vjl | W94 | Dipeptidyl peptidase 4 | / | 0.444 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.444 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.443 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.443 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.443 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.443 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.443 | |
| 4nes | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.443 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.442 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.442 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.442 | |
| 2qc8 | ADP | Glutamine synthetase | 6.3.1.2 | 0.442 | |
| 3d3x | ARG_ILE_MET_GLU_NH2 | Type E botulinum toxin | / | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 4qak | 2AM | RNA 2',3'-cyclic phosphodiesterase | / | 0.442 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.442 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.441 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.441 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.441 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.441 | |
| 2nvk | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.441 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.441 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.441 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 2yqz | SAM | Uncharacterized protein | / | 0.441 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.441 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4jic | FMN | GTN Reductase | / | 0.441 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.440 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.440 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.440 | |
| 3c8a | ARG_ARG_GLY_LEU_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.440 | |
| 3faz | NOS | Purine nucleoside phosphorylase | / | 0.440 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.440 | |
| 4l4x | NDP | AmphI | / | 0.440 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.440 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.440 |