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 |
|---|---|---|---|
| 4oi4 | ATP | mRNA cleavage and polyadenylation factor CLP1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4oi4 | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 1.000 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.550 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.502 | |
| 4e2d | FMN | Dehydrogenase | / | 0.485 | |
| 3ivm | ZPR | Prolyl endopeptidase | / | 0.478 | |
| 4e2b | FMN | Dehydrogenase | / | 0.474 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.472 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.471 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.470 | |
| 2x3j | ATP | AcsD | / | 0.469 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.468 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.467 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.467 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.465 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.464 | |
| 1ryd | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.463 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.463 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.463 | |
| 3oes | GNP | GTPase RhebL1 | / | 0.462 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.461 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.461 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.460 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.460 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.459 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.458 | |
| 4jic | FMN | GTN Reductase | / | 0.458 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.457 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.457 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.457 | |
| 5cfp | C2E | Stimulator of interferon genes protein | / | 0.457 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.456 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.456 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.456 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.455 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.455 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.454 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.454 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.454 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.454 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.453 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.453 | |
| 4e2x | TYD | Methyltransferase | / | 0.453 | |
| 4qq3 | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.453 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.453 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.452 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.452 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4qec | NAP | ElxO | / | 0.452 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.451 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.451 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.451 | |
| 3mzh | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.451 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.451 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.450 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.450 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.450 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.450 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.449 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.449 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.449 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.448 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.448 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.447 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.447 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.447 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.447 | |
| 3ukf | GDU | UDP-galactopyranose mutase | / | 0.447 | |
| 4j2w | FAD | Kynurenine 3-monooxygenase | / | 0.447 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.446 | |
| 1sb9 | UPG | WbpP | / | 0.446 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.446 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.446 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.446 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.446 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.445 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.445 | |
| 3opm | LUI | Dipeptidyl peptidase 4 | / | 0.445 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.445 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.445 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.444 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.444 | |
| 2x92 | X92 | Angiotensin-converting enzyme | 3.4.15.1 | 0.444 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.444 | |
| 3daa | PDD | D-alanine aminotransferase | 2.6.1.21 | 0.444 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.444 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.444 | |
| 1s63 | 778 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.442 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 2af6 | FAD | Flavin-dependent thymidylate synthase | 2.1.1.148 | 0.442 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.442 | |
| 4e2z | JHZ | Methyltransferase | / | 0.442 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.442 | |
| 4nes | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.442 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.442 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.441 | |
| 1s4o | GDP | Glycolipid 2-alpha-mannosyltransferase | / | 0.441 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.441 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 3ge6 | FMN | Nitroreductase | / | 0.441 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.441 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.441 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.441 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.440 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.440 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.440 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.440 |