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 |
|---|---|---|---|
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.773 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.765 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.671 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.643 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.557 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.534 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.509 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.495 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.484 | |
| 2ejz | SAH | Diphthine synthase | / | 0.482 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.473 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.463 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.462 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.461 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.461 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.456 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.454 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.453 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.452 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.452 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.451 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.451 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.449 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.449 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.449 | |
| 2yhu | WHF | Pteridine reductase | / | 0.448 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4qfy | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.448 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.447 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.447 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.447 | |
| 1c7o | PPG | Hemolysin | / | 0.446 | |
| 1fml | RTL | Retinol dehydratase | / | 0.446 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.446 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.446 | |
| 1jdz | FMB | Purine nucleoside phosphorylase | / | 0.445 | |
| 1rvv | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.445 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.445 | |
| 2v57 | PRL | TetR family transcriptional regulator | / | 0.445 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.445 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.444 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.444 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.441 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.440 | |
| 4j7h | TRH | PCZA361.3 | / | 0.440 |