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 |
|---|---|---|---|
| 2clm | F6F | Tryptophan synthase alpha chain |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2clm | F6F | Tryptophan synthase alpha chain | / | 1.000 | |
| 2clf | F6F | Tryptophan synthase alpha chain | / | 0.704 | |
| 4y6g | F6F | Tryptophan synthase alpha chain | / | 0.676 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.619 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.615 | |
| 1k8z | IAG | Tryptophan synthase alpha chain | / | 0.581 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.542 | |
| 1kfc | IPL | Tryptophan synthase alpha chain | / | 0.526 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.520 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.490 | |
| 1k8y | 13P | Tryptophan synthase alpha chain | / | 0.488 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.487 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.486 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.486 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.486 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.485 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.479 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.476 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.475 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.475 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.473 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.472 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.471 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.471 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.469 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.468 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.468 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.467 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.467 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.467 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.466 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.466 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.466 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.465 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.465 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.464 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.463 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.463 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.462 | |
| 2ejz | SAH | Diphthine synthase | / | 0.462 | |
| 1fml | RTL | Retinol dehydratase | / | 0.461 | |
| 1n75 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.461 | |
| 1std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.461 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.461 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.461 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3eku | CY9 | Actin-5C | / | 0.460 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.460 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.459 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.459 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4x7w | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.458 | |
| 4y38 | 0A9 | Endothiapepsin | 3.4.23.22 | 0.458 | |
| 5dp2 | NAP | CurF | / | 0.458 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.457 | |
| 3klb | FMN | Uncharacterized protein | / | 0.457 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3eks | CY9 | Actin-5C | / | 0.456 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.456 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 2iwh | ANP | Elongation factor 3A | / | 0.455 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.455 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.455 | |
| 1a5b | IGP | Tryptophan synthase alpha chain | / | 0.454 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.454 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.454 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4j7g | TRH | PCZA361.3 | / | 0.454 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.453 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.453 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.453 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.453 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.453 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.453 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.452 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.452 | |
| 1txz | APR | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.452 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.452 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.452 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.451 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.451 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4x81 | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.451 | |
| 1a9c | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.450 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.450 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.450 | |
| 2ym2 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.450 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.450 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.450 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.450 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.449 | |
| 1krr | ACO | Galactoside O-acetyltransferase | 2.3.1.18 | 0.449 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.449 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.449 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.449 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.448 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.447 | |
| 2cv1 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.447 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.447 | |
| 2rgj | FAD | Flavin-containing monooxygenase | / | 0.447 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 2dxi | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.446 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.446 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2v00 | V15 | Endothiapepsin | 3.4.23.22 | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.446 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.446 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.446 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.446 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1u0w | STL | Chalcone synthase 2 | 2.3.1.74 | 0.445 | |
| 2fxu | BID | Actin, alpha skeletal muscle | / | 0.445 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.445 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.445 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.445 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.445 | |
| 1c7o | PPG | Hemolysin | / | 0.444 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.444 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.444 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.444 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.444 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.444 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.444 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.444 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.444 | |
| 4lut | DCS | Alanine racemase | / | 0.444 | |
| 4x7v | MIV | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.444 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.443 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.443 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.443 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.443 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.443 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.443 | |
| 1a5s | FIP | Tryptophan synthase alpha chain | / | 0.442 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.442 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.442 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.442 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.442 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.442 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4l7h | 1W1 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.441 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.441 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.441 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.441 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.441 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 3ogx | H1S | Peptidoglycan recognition protein 1 | / | 0.441 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.441 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.441 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.440 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.440 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.440 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.440 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4eu4 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.440 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.440 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.440 |