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 |
|---|---|---|---|
| 3mau | PLR | Putative sphingosine-1-phosphate lyase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 1.000 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.664 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.493 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.493 | |
| 4h6p | FMN | Chromate reductase | / | 0.493 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.488 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.487 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.486 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.480 | |
| 1rft | PXM | Pyridoxal kinase | 2.7.1.35 | 0.479 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.476 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.476 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.471 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.471 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.471 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.469 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.468 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.468 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.468 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.468 | |
| 4lay | I63 | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.468 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.465 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.464 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.464 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.464 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.463 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.463 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.463 | |
| 1n95 | FTH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.462 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.461 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.460 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.460 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.459 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.459 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.459 | |
| 3x2e | NAI | Adenosylhomocysteinase | / | 0.459 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.458 | |
| 3ebl | GA4 | Gibberellin receptor GID1 | / | 0.458 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.458 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.458 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.457 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.456 | |
| 2yim | MC4 | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.456 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.456 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.455 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.455 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.455 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.455 | |
| 4dja | FAD | (6-4) photolyase | / | 0.455 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.454 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.454 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.454 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.454 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.454 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.454 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.454 | |
| 1i9c | 5AD | Glutamate mutase epsilon subunit | / | 0.453 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.453 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.453 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 3p5p | A3C | Taxadiene synthase | 4.2.3.17 | 0.452 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.451 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 4phl | PIL | Phosphodiesterase | / | 0.451 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.450 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.450 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.450 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.450 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.450 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.450 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.450 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.450 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.449 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.449 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.449 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.448 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.448 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.448 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.447 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.447 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.447 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.447 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.447 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.447 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.446 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.446 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3v2u | ATP | Protein GAL3 | / | 0.446 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.446 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.446 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.446 | |
| 3fvu | IAC | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.445 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.445 | |
| 1gax | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.444 | |
| 1nl4 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.444 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.444 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3jus | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.444 | |
| 4u16 | 3C0 | Muscarinic acetylcholine receptor M3 | / | 0.444 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.443 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2dg4 | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2vd7 | PD2 | Lysine-specific demethylase 4A | 1.14.11 | 0.443 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.443 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.443 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.443 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.443 | |
| 4wfr | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.442 | |
| 1l7x | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.442 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.442 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.442 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 4drm | 0MC | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.442 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.441 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.441 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4dxl | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.441 | |
| 4x7w | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.441 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.440 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.440 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.440 | |
| 2vtd | LKM | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.440 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.440 | |
| 3hl4 | CDC | Choline-phosphate cytidylyltransferase A | / | 0.440 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.440 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.440 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.440 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.440 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.440 |