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 |
|---|---|---|---|
| 2zvb | SAH | Precorrin-3 C17-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 1.000 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.580 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.543 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.491 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.489 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.482 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.480 | |
| 4yvz | 3AT | DNA integrity scanning protein DisA | / | 0.480 | |
| 2dsg | SAH | Diphthine synthase | / | 0.476 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.475 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.474 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.474 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.473 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.472 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.472 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.471 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.469 | |
| 1wng | SAH | Diphthine synthase | / | 0.466 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.466 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.464 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.464 | |
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.463 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.463 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.463 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.463 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.463 | |
| 2e07 | SAH | Diphthine synthase | / | 0.462 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.461 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.461 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.461 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.461 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.460 | |
| 2dek | SAH | Diphthine synthase | / | 0.460 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.460 | |
| 3ahn | 3A1 | Oligopeptidase | / | 0.460 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.460 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.458 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.458 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.458 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.458 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.457 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.457 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.457 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.457 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.457 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.457 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.456 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.456 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.455 | |
| 3int | FDA | UDP-galactopyranose mutase | 5.4.99.9 | 0.454 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.454 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.453 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.453 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.453 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.453 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.452 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4jic | FMN | GTN Reductase | / | 0.452 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.451 | |
| 2emr | SAH | Diphthine synthase | / | 0.451 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.451 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.451 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.451 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.451 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.451 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.450 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.450 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.450 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.450 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.450 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.450 | |
| 2huq | SAH | Diphthine synthase | / | 0.450 | |
| 2z6r | SAH | Diphthine synthase | / | 0.450 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.450 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.450 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1v0j | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.449 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.449 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.449 | |
| 2e17 | SAH | Diphthine synthase | / | 0.449 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.449 | |
| 2ii6 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.449 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.449 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.449 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.449 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.449 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.449 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.449 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.448 | |
| 2e15 | SAH | Diphthine synthase | / | 0.448 | |
| 2e4n | SAH | Diphthine synthase | / | 0.448 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.448 | |
| 2ejk | SAH | Diphthine synthase | / | 0.448 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.448 | |
| 3aho | 3A2 | Oligopeptidase | / | 0.448 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.448 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.448 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.448 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.448 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.448 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.448 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.447 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.447 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.447 | |
| 2dxx | SAH | Diphthine synthase | / | 0.447 | |
| 2owk | SAH | Diphthine synthase | / | 0.447 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.447 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.447 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.447 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.447 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.446 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.446 | |
| 2dsh | SAH | Diphthine synthase | / | 0.446 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.446 | |
| 2ehl | SAH | Diphthine synthase | / | 0.446 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.446 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.446 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.446 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.446 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.446 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.445 | |
| 2e8q | SAH | Diphthine synthase | / | 0.445 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.445 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.445 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.445 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.445 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.445 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.444 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.444 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.444 | |
| 2eeq | SAH | Diphthine synthase | / | 0.444 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.444 | |
| 2pck | SAH | Diphthine synthase | / | 0.444 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.444 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.444 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.444 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.443 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.443 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.443 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.443 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.443 | |
| 4ikz | AFS | Di-tripeptide ABC transporter (Permease) | / | 0.443 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.443 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.442 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.442 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.442 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.442 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 2el0 | SAH | Diphthine synthase | / | 0.442 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.442 | |
| 3rfa | SAM | Dual-specificity RNA methyltransferase RlmN | / | 0.442 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.442 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.442 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.442 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2cwf | NDP | Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase | / | 0.441 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.441 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 1ri1 | GTG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.440 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.440 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.440 | |
| 2egb | SAH | Diphthine synthase | / | 0.440 | |
| 2p5f | SAH | Diphthine synthase | / | 0.440 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.440 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 |