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 |
|---|---|---|---|
| 3vw7 | VPX | Proteinase-activated receptor 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 1.000 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.498 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.492 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.492 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.487 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.485 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.482 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.480 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.479 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.477 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.475 | |
| 3zuy | TCH | Transporter | / | 0.474 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.471 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.469 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.468 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.467 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.466 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.466 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.463 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.462 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.462 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.462 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.461 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.460 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.459 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.459 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.459 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.459 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.459 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.458 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.458 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.457 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.457 | |
| 3anm | SYD | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.457 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.457 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.457 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.456 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.456 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.456 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.455 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.455 | |
| 2h3w | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.455 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.455 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.455 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.455 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.455 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.454 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.453 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2bac | FAD | Putative aminooxidase | / | 0.453 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.453 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.452 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.452 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.451 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.451 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.450 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.450 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.449 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.449 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.449 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.449 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.449 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.449 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.449 | |
| 2d4v | NAD | Isocitrate dehydrogenase [NADP] | / | 0.448 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.448 | |
| 3dr8 | ACO | L-methionine sulfoximine/L-methionine sulfone acetyltransferase | / | 0.448 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.448 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.448 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.448 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.448 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.448 | |
| 4feh | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.448 | |
| 5dp2 | NAP | CurF | / | 0.448 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.447 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.447 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.447 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.447 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.447 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.447 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.447 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.447 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.446 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3f6s | FMN | Flavodoxin | / | 0.446 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.446 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.446 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 1r2j | FAD | FkbI | / | 0.445 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.445 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.445 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.445 | |
| 4h1q | 0XX | Matrix metalloproteinase-9 | 3.4.24.35 | 0.445 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.445 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.444 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.444 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 2yim | MC4 | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.444 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.444 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.443 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.443 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.443 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.443 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.443 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.443 | |
| 4dpl | NAP | Malonyl-CoA reductase | 1.2.1.75 | 0.443 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.443 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.442 | |
| 1tl7 | ONM | Adenylate cyclase type 2 | / | 0.442 | |
| 1tl7 | ONM | Adenylate cyclase type 5 | / | 0.442 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.442 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.442 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.441 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.441 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.441 | |
| 3ieu | GDP | GTPase Era | / | 0.441 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.441 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.441 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1ld8 | U49 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.440 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.440 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.440 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3r96 | ACO | MccE protein | / | 0.440 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.440 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4kdr | SAH | Ubiquinone biosynthesis O-methyltransferase | / | 0.440 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.440 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.440 |