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 |
|---|---|---|---|
| 3gon | ANP | Phosphomevalonate kinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3gon | ANP | Phosphomevalonate kinase | / | 1.000 | |
| 4yvz | 3AT | DNA integrity scanning protein DisA | / | 0.493 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.491 | |
| 1p9w | ANP | Type II secretion system protein E | / | 0.485 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.485 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.481 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.480 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.475 | |
| 2avv | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.472 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.471 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.469 | |
| 4a0r | DTB | Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial | 6.3.3.3 | 0.469 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.468 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.468 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.468 | |
| 1jdt | MTA | Purine nucleoside phosphorylase | / | 0.466 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.466 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.466 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.465 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.462 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.462 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.461 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.460 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.460 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.460 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.459 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.459 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.458 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.458 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.458 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.457 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.457 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.457 | |
| 3i7e | DJR | Gag-Pol polyprotein | / | 0.456 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 1bwb | 146 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.454 | |
| 2pwc | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.454 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.454 | |
| 1r6t | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.453 | |
| 2uzf | CAA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.453 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.453 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.452 | |
| 4z36 | ON3 | Lysophosphatidic acid receptor 1 | / | 0.452 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.451 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.451 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.450 | |
| 4y9q | C2E | Uncharacterized protein | / | 0.450 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.449 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 3r9i | ADP | Septum site-determining protein MinD | / | 0.449 | |
| 3w8r | ACP | Uridine kinase | / | 0.449 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.449 | |
| 1lvl | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.448 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.448 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.448 | |
| 4fry | NAD | Putative signal-transduction protein with CBS domains | / | 0.448 | |
| 1xnj | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1 | 2.7.1.25 | 0.447 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.447 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.447 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.447 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.446 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.446 | |
| 1bv9 | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.445 | |
| 1sgu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.445 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.445 | |
| 2onm | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.445 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 3zhb | NAP | Putative dehydrogenase | / | 0.445 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.445 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.445 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.445 | |
| 1d4j | MSC | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.444 | |
| 1t7k | BH0 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.444 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.444 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.444 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.444 | |
| 1p4a | PCP | Pur operon repressor | / | 0.443 | |
| 1ytm | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.443 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.443 | |
| 2olr | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.443 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.443 | |
| 3dog | NNN | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 3wsj | MK1 | Protease | / | 0.443 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4nak | PBQ | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic | 2.7.7.60 | 0.443 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.442 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.442 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.442 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.442 | |
| 2fre | FMN | NAD(P)H-flavin oxidoreductase | / | 0.442 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.442 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4gn6 | TYL | Lactoperoxidase | 1.11.1.7 | 0.442 | |
| 4ki0 | ANP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.442 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.442 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.441 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.441 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 1b5d | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.440 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.440 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.440 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.440 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.440 | |
| 3ld6 | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.440 | |
| 3rai | X85 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.440 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.440 |