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 |
|---|---|---|---|
| 2z1w | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2z1w | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 1.000 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.639 | |
| 1q63 | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.631 | |
| 1f3e | DPZ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.593 | |
| 4hvx | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.581 | |
| 4hsh | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.565 | |
| 4gh3 | 0EV | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.557 | |
| 1efz | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.552 | |
| 3gc4 | AAQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.550 | |
| 3sm0 | AEK | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.547 | |
| 4gh1 | 0WX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.544 | |
| 1k4h | APQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.542 | |
| 4hqv | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.540 | |
| 3gc5 | 2MQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.534 | |
| 1n2v | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.533 | |
| 4fps | 0UX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.529 | |
| 3ge7 | AFQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.523 | |
| 2bbf | 344 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.518 | |
| 1pxg | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.517 | |
| 4q8p | CKR | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.513 | |
| 2qzr | S79 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.505 | |
| 1ozq | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.498 | |
| 4giy | 0WY | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.498 | |
| 1y5x | E89 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.496 | |
| 4h7z | GUN | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.487 | |
| 1q4w | DQU | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.484 | |
| 4gg9 | 0WW | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.481 | |
| 4gcx | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.480 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.479 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.478 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.478 | |
| 4gkh | 0J9 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.476 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.475 | |
| 3cow | 52H | Pantothenate synthetase | 6.3.2.1 | 0.475 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.473 | |
| 3bll | BPQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.472 | |
| 1vbn | YSA | Tyrosine--tRNA ligase | 6.1.1.1 | 0.471 | |
| 4fr1 | 0V2 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.471 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 1y5w | NEZ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.469 | |
| 3ts1 | TYA | Tyrosine--tRNA ligase | 6.1.1.1 | 0.467 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.466 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.465 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.465 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.463 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.462 | |
| 2z1x | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.462 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 4j7g | TRH | PCZA361.3 | / | 0.462 | |
| 2io6 | 330 | Wee1-like protein kinase | 2.7.10.2 | 0.461 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.460 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.459 | |
| 2b51 | UTP | RNA editing complex protein MP57 | / | 0.459 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.459 | |
| 4few | PP2 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.459 | |
| 4h6p | FMN | Chromate reductase | / | 0.459 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.459 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.459 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.458 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.457 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.457 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.457 | |
| 3arv | SAU | Chitinase A | / | 0.456 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.456 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.456 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.455 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.455 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.455 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.454 | |
| 1z5u | CMP | Class B acid phosphatase | / | 0.453 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.453 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.453 | |
| 1i59 | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.452 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 5doz | NDP | JamJ | / | 0.452 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.451 | |
| 3coz | 54H | Pantothenate synthetase | 6.3.2.1 | 0.450 | |
| 3zo7 | K6H | Muconolactone Delta-isomerase | / | 0.450 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.449 | |
| 1s4d | SAH | Uroporphyrinogen-III C-methyltransferase | 2.1.1.107 | 0.449 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.449 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.448 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4gkt | 0O1 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.448 | |
| 1ybg | TAV | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.447 | |
| 3oez | STI | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.447 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.447 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1zdw | FLV | Prenyltransferase | / | 0.446 | |
| 2xtb | KRM | Adenosine kinase, putative | / | 0.446 | |
| 3mte | SAM | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.446 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.446 | |
| 3zxi | TYA | Tyrosine--tRNA ligase, mitochondrial | 6.1.1.1 | 0.446 | |
| 4deg | 0JJ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.446 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.446 | |
| 5hg0 | SAM | Pantothenate synthetase | / | 0.446 | |
| 5je3 | SAH | Methyl transferase | / | 0.446 | |
| 5d6l | CAU | Beta-2 adrenergic receptor | / | 0.446 | |
| 1pke | 2FD | Purine nucleoside phosphorylase DeoD-type | / | 0.445 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.445 | |
| 3occ | DIH | Purine nucleoside phosphorylase DeoD-type | / | 0.445 | |
| 4qpp | SAH | Protein arginine N-methyltransferase 6 | / | 0.445 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.444 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.444 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.444 | |
| 2ejz | SAH | Diphthine synthase | / | 0.444 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.444 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.444 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.444 | |
| 3n87 | N87 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.444 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.444 | |
| 4a0m | NAD | Betaine aldehyde dehydrogenase, chloroplastic | 1.2.1.8 | 0.444 | |
| 4x2q | NAD | Retinal dehydrogenase 2 | 1.2.1.36 | 0.444 | |
| 5f54 | TMP | Single-stranded-DNA-specific exonuclease | / | 0.444 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.443 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 3kp4 | MII | Transcriptional regulator TcaR | / | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4f3g | KAI | Glutamate receptor 3 | / | 0.443 | |
| 4fev | PP1 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.443 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.443 | |
| 4j55 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4ea3 | 0NN | Nociceptin receptor | / | 0.443 | |
| 1oqc | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.442 | |
| 1srj | NAB | Streptavidin | / | 0.442 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.442 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.442 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.442 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.442 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 1ez0 | NAP | NADP-dependent fatty aldehyde dehydrogenase | 1.2.1.4 | 0.441 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.441 | |
| 2cle | F6F | Tryptophan synthase alpha chain | / | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2jbl | SMA | Reaction center protein L chain | / | 0.441 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.441 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.441 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.441 | |
| 3vi5 | M4M | Hematopoietic prostaglandin D synthase | / | 0.441 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.441 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.441 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.441 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.440 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.440 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.440 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.440 | |
| 2pid | YSA | Tyrosine--tRNA ligase, mitochondrial | 6.1.1.1 | 0.440 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.440 |