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 |
|---|---|---|---|
| 3ccb | B2Y | Dipeptidyl peptidase 4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ccb | B2Y | Dipeptidyl peptidase 4 | / | 1.000 | |
| 3vjk | M51 | Dipeptidyl peptidase 4 | / | 0.674 | |
| 3vjl | W94 | Dipeptidyl peptidase 4 | / | 0.665 | |
| 3qbj | NXZ | Dipeptidyl peptidase 4 | / | 0.631 | |
| 3opm | LUI | Dipeptidyl peptidase 4 | / | 0.597 | |
| 3ccc | 7AC | Dipeptidyl peptidase 4 | / | 0.592 | |
| 3f8s | PF2 | Dipeptidyl peptidase 4 | / | 0.579 | |
| 2aj8 | SC3 | Dipeptidyl peptidase 4 | / | 0.574 | |
| 2rgu | 356 | Dipeptidyl peptidase 4 | / | 0.554 | |
| 4ffw | 715 | Dipeptidyl peptidase 4 | / | 0.541 | |
| 4g1f | 0WG | Dipeptidyl peptidase 4 | / | 0.535 | |
| 3g0b | T22 | Dipeptidyl peptidase 4 | / | 0.524 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.524 | |
| 2oae | AIL | Dipeptidyl peptidase 4 | / | 0.522 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.503 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.503 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.493 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.492 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.491 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.489 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.486 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.477 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.475 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.475 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.474 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.472 | |
| 3g0d | XIH | Dipeptidyl peptidase 4 | / | 0.472 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.471 | |
| 4qg1 | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.471 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.470 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.470 | |
| 3wqu | ATP | Cell division protein FtsA | / | 0.469 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.468 | |
| 3kyb | FMN | UDP-galactopyranose mutase | 5.4.99.9 | 0.468 | |
| 2c6c | 24I | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.467 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.467 | |
| 2x96 | RX3 | Angiotensin-converting enzyme | 3.4.15.1 | 0.467 | |
| 3o5r | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.467 | |
| 3g0c | RUF | Dipeptidyl peptidase 4 | / | 0.466 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.466 | |
| 4de2 | DN3 | Beta-lactamase | / | 0.466 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.465 | |
| 1qpl | 587 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.465 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.464 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.464 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.464 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.464 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.464 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.464 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.464 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.462 | |
| 4lut | DCS | Alanine racemase | / | 0.462 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.461 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.461 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.461 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.461 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.460 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.460 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.459 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.459 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.459 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.459 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.458 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.458 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.458 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.458 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.458 | |
| 3e6e | DCS | Alanine racemase | / | 0.457 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4j7h | TRH | PCZA361.3 | / | 0.457 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.456 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.456 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.456 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.456 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.455 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.455 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.455 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.455 | |
| 4de3 | DN8 | Beta-lactamase | / | 0.455 | |
| 4rxq | DUT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.455 | |
| 1mbb | EEB | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.454 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.454 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.454 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.453 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.453 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.453 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.453 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.453 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.452 | |
| 3zgz | 84T | Leucine--tRNA ligase | / | 0.452 | |
| 4bek | XK0 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.452 | |
| 4jay | NAP | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.452 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.451 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.451 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.451 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.450 | |
| 1acj | THA | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.449 | |
| 2jgb | MGT | Eukaryotic translation initiation factor 4E type 2 | / | 0.449 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.449 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.449 | |
| 1h66 | RH1 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.448 | |
| 1vfs | DCS | Alanine racemase | / | 0.448 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.448 | |
| 2cb3 | MLD | Peptidoglycan-recognition protein LE | / | 0.448 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.448 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.447 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.447 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.447 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.447 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.447 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3ukf | GDU | UDP-galactopyranose mutase | / | 0.447 | |
| 4dh0 | MR8 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.447 | |
| 4hn1 | TYD | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.447 | |
| 4lay | I63 | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.447 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.447 | |
| 2dg4 | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.446 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2zue | ANP | Arginine--tRNA ligase | 6.1.1.19 | 0.446 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.446 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.446 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.445 | |
| 1j37 | X8Z | Angiotensin-converting enzyme | 3.4.15.1 | 0.445 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.445 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.445 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.445 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.445 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.445 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.445 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.445 | |
| 4de1 | 0J6 | Beta-lactamase | / | 0.445 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.445 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1og4 | NAI | T-cell ecto-ADP-ribosyltransferase 2 | / | 0.444 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.444 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.444 | |
| 3ksl | SZH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.444 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.444 | |
| 4tny | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 1foa | UD1 | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | 2.4.1.101 | 0.443 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.443 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.443 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.443 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.442 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.442 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.442 | |
| 4ifn | 12O | Kelch-like ECH-associated protein 1 | / | 0.442 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.441 | |
| 2idv | M7G | Eukaryotic translation initiation factor 4E-1 | / | 0.441 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.441 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.441 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3v2u | ATP | Protein GAL3 | / | 0.441 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4dyb | 0MH | Nucleoprotein | / | 0.441 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.441 | |
| 4nv1 | TYD | Formyl transferase | / | 0.441 | |
| 5f54 | TMP | Single-stranded-DNA-specific exonuclease | / | 0.441 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.440 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.440 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.440 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.440 | |
| 3n71 | SFG | Histone-lysine N-methyltransferase Smyd1 | / | 0.440 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.440 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4kl1 | PCG | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.440 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.440 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.440 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.440 |