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 |
|---|---|---|---|
| 3vv0 | KH3 | Histone-lysine N-methyltransferase SETD7 | 2.1.1.43 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3vv0 | KH3 | Histone-lysine N-methyltransferase SETD7 | 2.1.1.43 | 1.000 | |
| 3vuz | K15 | Histone-lysine N-methyltransferase SETD7 | 2.1.1.43 | 0.577 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.480 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.476 | |
| 3nxq | RX4 | Angiotensin-converting enzyme | 3.2.1 | 0.476 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.476 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.473 | |
| 5dp2 | NAP | CurF | / | 0.473 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.472 | |
| 1n6c | SAM | Histone-lysine N-methyltransferase SETD7 | 2.1.1.43 | 0.471 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.469 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.469 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 4kqq | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.469 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.468 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.468 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.467 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.467 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.466 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.465 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.465 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.465 | |
| 2x97 | RX4 | Angiotensin-converting enzyme | 3.4.15.1 | 0.463 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.462 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.461 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.461 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.461 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.460 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.459 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.459 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.459 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.459 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.458 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.458 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.457 | |
| 3bmo | NAP | Pteridine reductase | / | 0.457 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.456 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.456 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4bxk | 1IU | Angiotensin-converting enzyme | 3.2.1 | 0.455 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2x92 | X92 | Angiotensin-converting enzyme | 3.4.15.1 | 0.453 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.453 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.453 | |
| 1v0j | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.452 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.452 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.452 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.452 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.450 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.450 | |
| 2bqz | SAH | N-lysine methyltransferase KMT5A | / | 0.450 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.450 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.450 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.449 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.449 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.449 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 2ck3 | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.448 | |
| 2ck3 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.448 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.448 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.448 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.447 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.447 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3vx4 | ATP | Putative ABC transporter, ATP-binding protein ComA | / | 0.447 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.446 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.446 | |
| 3int | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.446 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.446 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.445 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.445 | |
| 2x95 | X95 | Angiotensin-converting enzyme | 3.4.15.1 | 0.445 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4blr | UTP | NTPase P4 | / | 0.445 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.445 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.444 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.444 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3ukf | GDU | UDP-galactopyranose mutase | / | 0.444 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.444 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.443 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.443 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1req | DCA | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.442 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3ahn | 3A1 | Oligopeptidase | / | 0.442 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4coj | CTP | Uncharacterized protein | / | 0.442 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1wam | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.441 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.441 | |
| 3d3x | ARG_ILE_MET_GLU_NH2 | Type E botulinum toxin | / | 0.441 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3w2f | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.441 | |
| 4xd1 | T3Q | Qdtf | / | 0.441 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.440 | |
| 3sgl | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 |