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 |
|---|---|---|---|
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 1.000 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.671 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.597 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.497 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.481 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.476 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.475 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.474 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.468 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.468 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.466 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.466 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.463 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.463 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.461 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.459 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3b9l | AZZ | Serum albumin | / | 0.458 | |
| 3hxc | BD6 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.458 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.458 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.457 | |
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 | 0.457 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.457 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.456 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.455 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.455 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.455 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.455 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.455 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.454 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.453 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.452 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.452 | |
| 3qw8 | CYS_ARG_GLY_CYS_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.452 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.450 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.450 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.450 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4gtt | 7TQ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.449 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.448 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.448 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.446 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.446 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4jbs | P52 | Endoplasmic reticulum aminopeptidase 2 | 3.4.11 | 0.446 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.445 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.445 | |
| 3fr2 | 8CA | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.444 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.444 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3eft | 3BS | Carbonic anhydrase 2 | 4.2.1.1 | 0.444 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.443 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.443 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.443 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.443 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.443 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.443 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.443 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.443 | |
| 4kqr | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.443 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.442 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.442 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.441 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.441 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.441 | |
| 3c89 | ARG_ARG_GLY_MET_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.441 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.441 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 1u1c | BAU | Uridine phosphorylase | 2.4.2.3 | 0.440 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.440 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3c8a | ARG_ARG_GLY_LEU_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.440 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.440 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.440 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 |