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 |
|---|---|---|---|
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 1.000 | |
| 3dz7 | O8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.779 | |
| 3h0v | M2T | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.663 | |
| 3dz2 | A8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.653 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.642 | |
| 3dz6 | M8E | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.625 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.576 | |
| 1i7m | CG | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.530 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.473 | |
| 2ejz | SAH | Diphthine synthase | / | 0.470 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.469 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.467 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.465 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.464 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.460 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.459 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.458 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.457 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.457 | |
| 1ahg | TYR_PLP | Aspartate aminotransferase | 2.6.1.1 | 0.456 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.456 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.456 | |
| 3icp | NAD | NAD-dependent epimerase/dehydratase | / | 0.456 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.456 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.456 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.454 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.453 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.453 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.451 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.451 | |
| 1jdt | MTA | Purine nucleoside phosphorylase | / | 0.450 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.450 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4x81 | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.450 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.449 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.449 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.449 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.449 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.449 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.449 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.448 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.448 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.448 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.448 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.447 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.446 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.446 | |
| 4j7g | TRH | PCZA361.3 | / | 0.446 | |
| 1zzu | DP1 | Nitric oxide synthase, brain | 1.14.13.39 | 0.445 | |
| 2v57 | PRL | TetR family transcriptional regulator | / | 0.445 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.445 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.444 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.444 | |
| 1fml | RTL | Retinol dehydratase | / | 0.443 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.443 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 3anm | SYD | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.442 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.442 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.442 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4hhy | 15R | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.441 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.441 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.441 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 |