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 |
|---|---|---|---|
| 2op1 | 8PC | Enoyl-ACP reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2op1 | 8PC | Enoyl-ACP reductase | / | 1.000 | |
| 2ol4 | JPN | Enoyl-ACP reductase | / | 0.919 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.491 | |
| 4n1g | CEI | Obelin | / | 0.491 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 4kxj | P34 | Nucleoprotein | / | 0.469 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.467 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.467 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.467 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.466 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.463 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.463 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.463 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.463 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.463 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.461 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.460 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.460 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.459 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.458 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.458 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.457 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.457 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.457 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.457 | |
| 3elm | 24F | Collagenase 3 | 3.4.24 | 0.456 | |
| 3i6r | J5Z | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.456 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.456 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.455 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.455 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.454 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.454 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.454 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.454 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.454 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.453 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.453 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.453 | |
| 4hai | I23 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.453 | |
| 4rrx | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.453 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.453 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1zdw | FLV | Prenyltransferase | / | 0.452 | |
| 2xvw | 9NR | Serum albumin | / | 0.452 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.452 | |
| 4v0s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.452 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.451 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.451 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.451 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.450 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.449 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.449 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.449 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.449 | |
| 1til | ATP | Anti-sigma F factor | / | 0.448 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.448 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.448 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.448 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.448 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.448 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.447 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.447 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.447 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.447 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.447 | |
| 1q23 | FUA | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.446 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.446 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.445 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.445 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.445 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.445 | |
| 4ys2 | 2BA | Uncharacterized protein | / | 0.445 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1n4q | LYS_CYS_VAL_ILE_LEU | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.444 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.444 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.444 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.444 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.444 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.444 | |
| 4y0k | NAP | AntE | / | 0.444 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.443 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.443 | |
| 2a9z | 26A | Adenosine kinase | 2.7.1.20 | 0.443 | |
| 2emu | SAH | Diphthine synthase | / | 0.443 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.443 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.443 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.443 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 4afg | QMR | Achbp | / | 0.443 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.442 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.442 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.442 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.442 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.442 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.442 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.442 | |
| 4iqq | D16 | Thymidylate synthase | / | 0.442 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.442 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1fm6 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.441 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 0.441 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.441 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.441 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4boe | CLR | Japanin | / | 0.441 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.441 | |
| 1olm | VTQ | SEC14-like protein 2 | / | 0.440 | |
| 1ya3 | STR | Mineralocorticoid receptor | / | 0.440 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.440 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.440 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3arv | SAU | Chitinase A | / | 0.440 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.440 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 3fnh | JPJ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.440 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.440 | |
| 4bw3 | 9BM | Bromodomain-containing protein 4 | / | 0.440 | |
| 4c6z | TLE | 3-oxoacyl-ACP synthase | / | 0.440 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.440 | |
| 5bvw | 1N1 | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.440 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.440 |