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 |
|---|---|---|---|
| 3nx2 | FER | Ferulic acid decarboxylase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3nx2 | FER | Ferulic acid decarboxylase | / | 1.000 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.502 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.492 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.489 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.489 | |
| 1eio | GCH | Gastrotropin | / | 0.485 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.485 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.485 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.484 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.482 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.482 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.479 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.474 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.474 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.472 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.472 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.471 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.470 | |
| 3tvx | PNX | cAMP-specific 3',5'-cyclic phosphodiesterase 4A | 3.1.4.53 | 0.468 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.467 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1c7o | PPG | Hemolysin | / | 0.466 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.466 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.465 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.465 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.462 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.462 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.461 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.461 | |
| 1q9m | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.459 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.458 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.458 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.458 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.457 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.456 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 3bjc | WAN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.455 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.455 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 1osv | CHC | Bile acid receptor | / | 0.454 | |
| 3g4l | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.454 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.453 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.453 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.451 | |
| 1vgq | CAO | Formyl-CoA:oxalate CoA-transferase | / | 0.451 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.451 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.450 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.450 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.449 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.449 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.446 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.446 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.446 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.446 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.446 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.445 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.444 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.444 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.444 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.444 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.444 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.443 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.443 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
| 1xkd | NAP | Isocitrate dehydrogenase [NADP] | / | 0.442 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.442 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.440 |