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 |
|---|---|---|---|
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 1.000 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.616 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.596 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.568 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.567 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.553 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.548 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.521 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.519 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.488 | |
| 1cne | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.483 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.473 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.471 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.470 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.468 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.467 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.467 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.463 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.462 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.462 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.461 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.461 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.460 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.459 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.458 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 3suf | SUE | Polyprotein | / | 0.456 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.456 | |
| 3eku | CY9 | Actin-5C | / | 0.455 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.455 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.454 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.454 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.453 | |
| 4qfy | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.453 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.453 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.452 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.452 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.452 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.451 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.451 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.450 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.449 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.449 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.449 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.448 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.448 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.448 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.448 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.448 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.447 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.446 | |
| 3eks | CY9 | Actin-5C | / | 0.445 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.445 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.442 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.442 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.440 | |
| 1ld7 | U66 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 |