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 |
|---|---|---|---|
| 3ewd | MCF | Adenosine deaminase, putative |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ewd | MCF | Adenosine deaminase, putative | / | 1.000 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.495 | |
| 2r5n | TPP | Transketolase 1 | / | 0.490 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.487 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.486 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.485 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.485 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.484 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.484 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.484 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.480 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.479 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.478 | |
| 4ear | IM5 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.476 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.474 | |
| 2yhu | WHF | Pteridine reductase | / | 0.474 | |
| 3upt | TPP | Transketolase | / | 0.474 | |
| 1trk | TPP | Transketolase 1 | 2.2.1.1 | 0.473 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.473 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.471 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 4jda | A9S | Abscisic acid receptor PYL3 | / | 0.470 | |
| 1fkw | PUR | Adenosine deaminase | 3.5.4.4 | 0.469 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.469 | |
| 2zi5 | 3L1 | Deoxycytidine kinase | 2.7.1.74 | 0.469 | |
| 1tkb | N1T | Transketolase 1 | 2.2.1.1 | 0.468 | |
| 3iel | U5P | Ribonuclease TTHA0252 | 3.1 | 0.468 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.467 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 1swe | BTN | Streptavidin | / | 0.466 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.465 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.464 | |
| 1zdw | FLV | Prenyltransferase | / | 0.464 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.462 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.461 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.461 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.460 | |
| 3v2u | ATP | Protein GAL3 | / | 0.460 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.459 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.458 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.458 | |
| 4x7v | MIV | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.458 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.458 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.457 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.457 | |
| 4lde | P0G | Beta-2 adrenergic receptor | / | 0.457 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.456 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 3vmm | P0D | Alanine--anticapsin ligase | / | 0.456 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.455 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.455 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.454 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2y3f | BTN | Streptavidin | / | 0.454 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.453 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.453 | |
| 1nbu | PH2 | Dihydroneopterin aldolase | / | 0.452 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.452 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.452 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.451 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.450 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.450 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.449 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.449 | |
| 1sre | HAB | Streptavidin | / | 0.449 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.448 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.448 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.448 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.448 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.448 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.447 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.447 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1mra | APG | Mandelate racemase | / | 0.446 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.446 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.446 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 1dtp | APU | Diphtheria toxin | / | 0.445 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.445 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.445 | |
| 1sri | DMB | Streptavidin | / | 0.445 | |
| 1uhh | CZP | Aequorin-2 | / | 0.445 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.445 | |
| 1xh5 | R68 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.445 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.445 | |
| 4nbj | D3Y | D-tyrosyl-tRNA(Tyr) deacylase | / | 0.445 | |
| 3d4s | TIM | Beta-2 adrenergic receptor | / | 0.445 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 3arv | SAU | Chitinase A | / | 0.444 | |
| 3nmn | PYV | Abscisic acid receptor PYL1 | / | 0.444 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3wzn | BTN | Streptavidin | / | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4nqg | CZH | Mitrocomin | / | 0.444 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.443 | |
| 1swn | BTN | Streptavidin | / | 0.443 | |
| 2r8o | T5X | Transketolase 1 | / | 0.443 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 5fsi | 8DG | 7,8-dihydro-8-oxoguanine triphosphatase | 3.6.1.55 | 0.443 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.443 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.442 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.442 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.442 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.442 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.442 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3ogk | OGK | Coronatine-insensitive protein 1 | / | 0.441 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.441 | |
| 1db5 | 6IN | Phospholipase A2, membrane associated | / | 0.440 | |
| 1lbb | KAI | Glutamate receptor 2 | / | 0.440 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.440 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.440 | |
| 1v7a | FRC | Adenosine deaminase | 3.5.4.4 | 0.440 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 2p1t | 3TN | Retinoic acid receptor RXR-alpha | / | 0.440 | |
| 2yat | EEU | Estrogen receptor | / | 0.440 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3jq7 | DX2 | Pteridine reductase, putative | / | 0.440 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.440 | |
| 3myt | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.440 | |
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.440 | |
| 4jq3 | ZOM | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.440 |