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 |
|---|---|---|---|
| 2cbo | TH2 | Neocarzinostatin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2cbo | TH2 | Neocarzinostatin | / | 1.000 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.516 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.511 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.500 | |
| 4x9d | U5P | Uncharacterized protein MJ1435 | / | 0.496 | |
| 2ejz | SAH | Diphthine synthase | / | 0.494 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.488 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.488 | |
| 1c7o | PPG | Hemolysin | / | 0.484 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.482 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.482 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.481 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.480 | |
| 2po3 | T4K | 4-dehydrase | / | 0.476 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.476 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.475 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.474 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.474 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.471 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.471 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.470 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.470 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.470 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.470 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.470 | |
| 4yaw | 2AM | NADPH--cytochrome P450 reductase | / | 0.470 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.469 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 3klb | FMN | Uncharacterized protein | / | 0.468 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.468 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.466 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.465 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.465 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.465 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.465 | |
| 4bek | XK0 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.463 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.463 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.463 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.462 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.462 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.461 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.461 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.460 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.460 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.460 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 5dp2 | NAP | CurF | / | 0.460 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.459 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.459 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.459 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.459 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.459 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.459 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.458 | |
| 2aov | C2M | Histamine N-methyltransferase | 2.1.1.8 | 0.458 | |
| 2dsh | SAH | Diphthine synthase | / | 0.458 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 3zg6 | APR | NAD-dependent protein deacetylase sirtuin-6 | 3.5.1 | 0.458 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 2ozr | GG1 | Collagenase 3 | 3.4.24 | 0.457 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.457 | |
| 2zts | ADP | Uncharacterized protein | / | 0.457 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.457 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.457 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.457 | |
| 3jqr | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.457 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.457 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.456 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 2h21 | SAM | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.455 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.455 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.455 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.454 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.454 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.454 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.454 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.453 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.452 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.452 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.452 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.452 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.452 | |
| 4ise | 1FW | Glucokinase | 2.7.1.2 | 0.452 | |
| 1vp5 | NAP | Oxidoreductase, aldo/keto reductase family | / | 0.451 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4e2y | JHZ | Methyltransferase | / | 0.451 | |
| 4phl | PIL | Phosphodiesterase | / | 0.451 | |
| 4v2g | CTC | Tetracycline repressor protein class D | / | 0.451 | |
| 2vjm | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.450 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.450 | |
| 3pdn | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.450 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.450 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4e0u | 0MV | Cyclic dipeptide N-prenyltransferase | / | 0.450 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.450 | |
| 1q23 | FUA | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.449 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.449 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.449 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.449 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.449 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.449 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 4fri | DWA | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.448 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2gci | MRR | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.448 | |
| 4bfd | 8T3 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 1pua | COA | HAT A1 | / | 0.447 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.447 | |
| 1w87 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.447 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 2e07 | SAH | Diphthine synthase | / | 0.447 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.447 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.447 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.446 | |
| 3rl4 | 5GP | Metallophosphoesterase MPPED2 | 3.1 | 0.446 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.446 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.446 | |
| 4j0z | 1H5 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.445 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.445 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.445 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.445 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4glx | 0XS | DNA ligase | 6.5.1.2 | 0.445 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1rvv | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2dxi | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.444 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.444 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.444 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.444 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.444 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.444 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.444 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.444 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.443 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.443 | |
| 3v2u | ATP | Protein GAL3 | / | 0.443 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.443 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4j7h | TRH | PCZA361.3 | / | 0.443 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.443 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.443 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.443 | |
| 5dv2 | C5P | CCR4-NOT transcription complex subunit 6-like | 3.1.13.4 | 0.443 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.442 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.442 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.442 | |
| 2gpj | FAD | Siderophore-interacting protein | / | 0.442 | |
| 2o6h | INI | 6,7-dimethyl-8-ribityllumazine synthase 1 | 2.5.1.78 | 0.442 | |
| 2ohh | FMN | Type A flavoprotein FprA | 1 | 0.442 | |
| 2pch | SAH | Diphthine synthase | / | 0.442 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.442 | |
| 4dya | 0MF | Nucleoprotein | / | 0.442 | |
| 4lut | DCS | Alanine racemase | / | 0.442 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.441 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.441 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.441 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.441 | |
| 4jp9 | 1M5 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4l98 | LRG | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.441 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1pz0 | NAP | Protein IolS | 1.1.1 | 0.440 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 1v5y | 4HC | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.440 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.440 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.440 | |
| 3q7j | FBO | Tricorn protease-interacting factor F3 | 3.4.11 | 0.440 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.440 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 5doz | NDP | JamJ | / | 0.440 | |
| 4ami | G90 | Beta-1 adrenergic receptor | / | 0.440 |