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 |
|---|---|---|---|
| 3t64 | DU3 | Deoxyuridine 5'-triphosphate nucleotidohydrolase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3t64 | DU3 | Deoxyuridine 5'-triphosphate nucleotidohydrolase | / | 1.000 | |
| 3t70 | DU4 | Deoxyuridine 5'-triphosphate nucleotidohydrolase | / | 0.581 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.564 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.522 | |
| 4wrk | DUP | DUTPase | / | 0.507 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.498 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.488 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.484 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.483 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.483 | |
| 4de2 | DN3 | Beta-lactamase | / | 0.482 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.481 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.481 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.481 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.480 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.479 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.479 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.479 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.478 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.478 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.477 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.476 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.476 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.475 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.474 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.473 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.473 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.472 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.472 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.471 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.471 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.470 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.470 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.470 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.468 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.468 | |
| 2b3v | ACO | Diamine acetyltransferase 1 | / | 0.467 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.467 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.467 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.466 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.466 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.465 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.465 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.464 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.462 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.462 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.462 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.462 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.462 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.462 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.461 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.461 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.461 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.460 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.460 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.460 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.460 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.460 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.460 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.460 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.459 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.459 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.458 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.458 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.458 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.458 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.458 | |
| 1qpl | 587 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.457 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.457 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.456 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.456 | |
| 1snf | UMP | Deoxyuridine 5'-triphosphate nucleotidohydrolase | 3.6.1.23 | 0.455 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.455 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.455 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.455 | |
| 3kjg | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.454 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.454 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.454 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.454 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.454 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.454 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.454 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 2ilv | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.453 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.453 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.452 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.452 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.452 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.452 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.452 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.451 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.451 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.451 | |
| 3g0b | T22 | Dipeptidyl peptidase 4 | / | 0.451 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.451 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 2ejz | SAH | Diphthine synthase | / | 0.450 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.450 | |
| 3eks | CY9 | Actin-5C | / | 0.450 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.450 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.450 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.450 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.449 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.449 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.449 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.449 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3r96 | ACO | MccE protein | / | 0.449 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.448 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.448 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.448 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.448 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.448 | |
| 1ja0 | FAD | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.447 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.447 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.447 | |
| 3wid | NAP | Glucose 1-dehydrogenase | / | 0.447 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.447 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.446 | |
| 1vyq | DUX | Deoxyuridine 5'-triphosphate nucleotidohydrolase | / | 0.446 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.446 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.445 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.445 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.445 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.445 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.445 | |
| 3psy | RB9 | Endothiapepsin | 3.4.23.22 | 0.445 | |
| 4ca6 | 3EF | Angiotensin-converting enzyme | 3.2.1 | 0.445 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.445 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.444 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.444 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2oke | DUP | DUTP pyrophosphatase | / | 0.444 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.444 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3a3g | DLZ | Lumazine protein | / | 0.444 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.444 | |
| 4ef4 | C2E | Stimulator of interferon genes protein | / | 0.444 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.443 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.443 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.443 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.443 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.443 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.443 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.443 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.443 | |
| 3tif | ADP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.443 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.443 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.443 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.442 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.442 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.442 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.442 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.442 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.442 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.441 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.441 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.441 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 2xyd | 3ES | Angiotensin-converting enzyme | 3.2.1 | 0.441 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3ho2 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.441 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4yp6 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.441 | |
| 5c4n | NAP | Precorrin-6A reductase | 1.3.1.54 | 0.441 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.440 | |
| 1pl1 | ABY | Glutathione S-transferase A1 | 2.5.1.18 | 0.440 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.440 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.440 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.440 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3iaa | TYD | CalG2 | / | 0.440 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4jiq | 1L5 | GTN Reductase | / | 0.440 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.440 | |
| 4lol | 1YE | Stimulator of interferon genes protein | / | 0.440 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.440 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.440 |