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 |
|---|---|---|---|
| 4e70 | N7I | Coniferyl alcohol 9-O-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4e70 | N7I | Coniferyl alcohol 9-O-methyltransferase | / | 1.000 | |
| 1xqc | AEJ | Estrogen receptor | / | 0.498 | |
| 1fdu | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.497 | |
| 2xke | WI2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.483 | |
| 4f79 | P53 | Putative phospho-beta-glucosidase | / | 0.483 | |
| 4xp4 | COC | Sodium-dependent dopamine transporter | / | 0.478 | |
| 3tam | M06 | Gag-Pol polyprotein | 2.7.7.49 | 0.477 | |
| 3rfm | CFF | Adenosine receptor A2a | / | 0.476 | |
| 2wqo | VGK | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.475 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.473 | |
| 2f4j | VX6 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.472 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.472 | |
| 2oh4 | GIG | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.471 | |
| 1df8 | BTN | Streptavidin | / | 0.470 | |
| 2rl5 | 2RL | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.470 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.470 | |
| 3tfj | THG | Dimethylsulfonioproprionate demethylase DmdA | 2.1.1.269 | 0.469 | |
| 1m52 | P17 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.468 | |
| 3cth | 319 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.468 | |
| 2xkf | BX1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.467 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.467 | |
| 4msk | 2C8 | Tankyrase-1 | 2.4.2.30 | 0.467 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.467 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.466 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.465 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.465 | |
| 4bch | T7Z | Cyclin-dependent kinase 9 | 2.7.11.22 | 0.465 | |
| 4bub | ADP | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase | / | 0.465 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.465 | |
| 3t1a | 5MA | Gag-Pol polyprotein | 2.7.7.49 | 0.464 | |
| 2z2w | 770 | Wee1-like protein kinase | 2.7.10.2 | 0.463 | |
| 4uog | YYY | Nucleoside diphosphate kinase | / | 0.463 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.462 | |
| 1w7k | ADP | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.462 | |
| 2opb | F21 | Phenylethanolamine N-methyltransferase | 2.1.1.28 | 0.462 | |
| 3e6o | A55 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.462 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.462 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.461 | |
| 2jle | I15 | Reverse transcriptase/RNaseH | / | 0.460 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.460 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.459 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.459 | |
| 3f82 | 353 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.459 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.459 | |
| 4jlt | 8PR | Cytochrome P450 2B4 | 1.14.14.1 | 0.459 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.459 | |
| 1sjw | NGV | Nogalonic acid methyl ester cyclase | / | 0.458 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.458 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.458 | |
| 4tyj | 0LI | Fibroblast growth factor receptor 4 | 2.7.10.1 | 0.458 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.458 | |
| 2b5j | 3AC | Gag-Pol polyprotein | 2.7.7.49 | 0.457 | |
| 3ldg | SAH | Uncharacterized protein | / | 0.457 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.457 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.457 | |
| 2gqg | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.456 | |
| 4i9i | 1DY | Tankyrase-1 | 2.4.2.30 | 0.456 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.455 | |
| 2io6 | 330 | Wee1-like protein kinase | 2.7.10.2 | 0.455 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.455 | |
| 3ewr | APR | Replicase polyprotein 1a | 3.4.22 | 0.455 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.455 | |
| 3lla | ACP | Myosin heavy chain kinase A | 2.7.11.7 | 0.455 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.454 | |
| 3e7t | B14 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.454 | |
| 3oez | STI | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.454 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.454 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 alpha chain | / | 0.453 | |
| 1kzu | RG1 | Light-harvesting protein B-800/850 beta chain | / | 0.453 | |
| 1uxu | NAP | NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase | / | 0.453 | |
| 3n65 | XFJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.453 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4ea1 | 3RX | Dehydrosqualene synthase | / | 0.453 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.453 | |
| 4rw6 | 494 | Gag-Pol polyprotein | 2.7.7.49 | 0.453 | |
| 1srf | MTB | Streptavidin | / | 0.452 | |
| 3qcz | ANP | Dihydrofolate synthase/folylpolyglutamate synthase | / | 0.452 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.452 | |
| 4m48 | 21B | Sodium-dependent dopamine transporter | / | 0.452 | |
| 4mmd | 29E | Na(+):neurotransmitter symporter (Snf family) | / | 0.452 | |
| 1qw5 | 14W | Nitric oxide synthase, inducible | 1.14.13.39 | 0.451 | |
| 2fb8 | 215 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.451 | |
| 2won | ZZE | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 3ar6 | 12D | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.451 | |
| 3tm0 | ANP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.451 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 1pr5 | TBN | Purine nucleoside phosphorylase DeoD-type | / | 0.450 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.450 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.450 | |
| 2v57 | PRL | TetR family transcriptional regulator | / | 0.450 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.450 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.450 | |
| 3e5a | VX6 | Aurora kinase A | 2.7.11.1 | 0.450 | |
| 3qpv | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.450 | |
| 4f1o | ACP | Probable serine/threonine-protein kinase roco4 | 2.7.11.1 | 0.450 | |
| 1qin | GIP | Lactoylglutathione lyase | 4.4.1.5 | 0.449 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.448 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.448 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.448 | |
| 3rey | XAC | Adenosine receptor A2a | / | 0.448 | |
| 1p33 | MTX | Pteridine reductase 1 | 1.5.1.33 | 0.447 | |
| 1zdw | FLV | Prenyltransferase | / | 0.447 | |
| 2yhu | WHF | Pteridine reductase | / | 0.447 | |
| 3sl8 | JN7 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 4ivq | I43 | Thymidine kinase | / | 0.447 | |
| 2x9v | TMQ | Pteridine reductase | / | 0.446 | |
| 3c6u | M22 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 3n1s | 5GP | Purine nucleoside phosphoramidase | / | 0.446 | |
| 4bjb | P34 | Tankyrase-2 | 2.4.2.30 | 0.446 | |
| 4gd9 | BTN | Streptavidin | / | 0.446 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.446 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.446 | |
| 4mmc | 29J | Na(+):neurotransmitter symporter (Snf family) | / | 0.446 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.446 | |
| 1kyz | FER | Caffeic acid 3-O-methyltransferase | 2.1.1.68 | 0.445 | |
| 1w22 | NHB | Histone deacetylase 8 | 3.5.1.98 | 0.445 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.445 | |
| 2xk4 | OL2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.445 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.445 | |
| 4uoh | ADP | Nucleoside diphosphate kinase | / | 0.445 | |
| 1o6r | R19 | Squalene--hopene cyclase | 4.2.1.129 | 0.444 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2c92 | TP6 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2hz4 | 4ST | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.444 | |
| 2imk | GTX | AGAP009194-PA | / | 0.444 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.444 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 1s2g | 3D1 | Nucleoside 2-deoxyribosyltransferase | / | 0.443 | |
| 2xk7 | 30E | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.443 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 3fzs | B96 | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.443 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.443 | |
| 4pl9 | ADP | Ethylene receptor 1 | / | 0.443 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 1a27 | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 2jav | 5Z5 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.442 | |
| 2xkd | T3M | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.442 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3gc8 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.442 | |
| 3q2j | CKI | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.442 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 4h4o | 506 | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1e2j | THM | Thymidine kinase | / | 0.441 | |
| 1v79 | FR7 | Adenosine deaminase | 3.5.4.4 | 0.441 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.441 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.441 | |
| 2etr | Y27 | Rho-associated protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3tfn | 2CJ | Dehydrosqualene synthase | / | 0.441 | |
| 4b8m | VX6 | Aurora kinase B-A | 2.7.11.1 | 0.441 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.441 | |
| 4fev | PP1 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.441 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.441 | |
| 1ly4 | COQ | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2xtb | KRM | Adenosine kinase, putative | / | 0.440 | |
| 2xwe | AMF | Glucosylceramidase | 3.2.1.45 | 0.440 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 3o9l | LPN | Renin | 3.4.23.15 | 0.440 | |
| 3w5e | NVW | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 |