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 |
|---|---|---|---|
| 3t0i | SAH | Putative methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3t0i | SAH | Putative methyltransferase | / | 1.000 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.596 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.572 | |
| 3kkz | SAM | Uncharacterized protein | / | 0.567 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.504 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.492 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.478 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.473 | |
| 4qtu | SAM | 18S rRNA (guanine(1575)-N(7))-methyltransferase | / | 0.473 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.473 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.471 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.471 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.471 | |
| 2yye | APC | Selenide, water dikinase | 2.7.9.3 | 0.469 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.469 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.468 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.467 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.463 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.462 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.460 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.460 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.460 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.460 | |
| 3wid | NAP | Glucose 1-dehydrogenase | / | 0.459 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2ehl | SAH | Diphthine synthase | / | 0.458 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.458 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.458 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.458 | |
| 1pr4 | MTP | Purine nucleoside phosphorylase DeoD-type | / | 0.456 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.456 | |
| 1xh5 | R68 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.456 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.456 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.456 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.455 | |
| 2ejz | SAH | Diphthine synthase | / | 0.454 | |
| 3g86 | T18 | Genome polyprotein | 2.7.7.48 | 0.454 | |
| 3mo0 | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.454 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.453 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.453 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.453 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.452 | |
| 4jt9 | 1NS | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.452 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.451 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.450 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.450 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.450 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.450 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1sve | I01 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.448 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1q23 | FUA | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.447 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.447 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.445 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.445 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.444 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3t7t | SAH | Uncharacterized protein | / | 0.444 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 2rh1 | CAU | Beta-2 adrenergic receptor | / | 0.444 | |
| 1xh8 | R55 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2dxi | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.443 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.443 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.443 | |
| 3v2u | ATP | Protein GAL3 | / | 0.443 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 1s63 | 778 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.442 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.442 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.442 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.442 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.442 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.441 | |
| 1vce | SAH | Diphthine synthase | / | 0.441 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.441 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.441 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.441 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.441 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.440 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.440 | |
| 4tta | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.440 |