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 |
|---|---|---|---|
| 3h4g | FID | Alcohol dehydrogenase [NADP(+)] | 1.1.1.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3h4g | FID | Alcohol dehydrogenase [NADP(+)] | 1.1.1.2 | 1.000 | |
| 2pd9 | FID | Aldose reductase | 1.1.1.21 | 0.550 | |
| 2pdw | FID | Aldose reductase | 1.1.1.21 | 0.549 | |
| 1pwm | FID | Aldose reductase | 1.1.1.21 | 0.548 | |
| 2f2k | TGG | Aldose reductase | 1.1.1.21 | 0.544 | |
| 3s3g | TLT | Aldose reductase | 1.1.1.21 | 0.541 | |
| 3fx4 | FX4 | Alcohol dehydrogenase [NADP(+)] | 1.1.1.2 | 0.533 | |
| 3u2c | SUZ | Aldose reductase | 1.1.1.21 | 0.530 | |
| 2is7 | 2CL | Aldose reductase | 1.1.1.21 | 0.524 | |
| 4gab | FID | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.523 | |
| 3cv7 | C2U | Alcohol dehydrogenase [NADP(+)] | 1.1.1.2 | 0.522 | |
| 3v35 | NTI | Aldose reductase | 1.1.1.21 | 0.514 | |
| 2pdk | SBI | Aldose reductase | 1.1.1.21 | 0.511 | |
| 3p2v | DOY | Aldose reductase | 1.1.1.21 | 0.505 | |
| 2pdy | FID | Aldose reductase | 1.1.1.21 | 0.504 | |
| 5liu | 388 | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.504 | |
| 1ef3 | FID | Aldose reductase | 1.1.1.21 | 0.503 | |
| 2agt | FID | Aldose reductase | 1.1.1.21 | 0.496 | |
| 1eko | I84 | Aldose reductase | 1.1.1.21 | 0.492 | |
| 2pdm | ZST | Aldose reductase | 1.1.1.21 | 0.490 | |
| 2pdi | ZST | Aldose reductase | 1.1.1.21 | 0.489 | |
| 1dlr | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.487 | |
| 2iej | S48 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.486 | |
| 1ah0 | SBI | Aldose reductase | 1.1.1.21 | 0.485 | |
| 2fzb | TOL | Aldose reductase | 1.1.1.21 | 0.485 | |
| 2ikj | 393 | Aldose reductase | 1.1.1.21 | 0.483 | |
| 2pdj | 393 | Aldose reductase | 1.1.1.21 | 0.481 | |
| 1zua | TOL | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.480 | |
| 2nvc | ITA | Aldose reductase | 1.1.1.21 | 0.480 | |
| 1el3 | I84 | Aldose reductase | 1.1.1.21 | 0.479 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.478 | |
| 4ga8 | SBI | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.478 | |
| 4wev | SUZ | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.478 | |
| 2ipw | 2CL | Aldose reductase | 1.1.1.21 | 0.477 | |
| 1az1 | ALR | Aldose reductase | 1.1.1.21 | 0.476 | |
| 3n61 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.475 | |
| 2vi5 | Y19 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.474 | |
| 3f3y | 4OA | Bile salt sulfotransferase | 2.8.2.14 | 0.474 | |
| 3ghr | LDT | Aldose reductase | 1.1.1.21 | 0.474 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.472 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.472 | |
| 2hvn | ZST | Aldose reductase | 1.1.1.21 | 0.471 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.468 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.468 | |
| 1us0 | LDT | Aldose reductase | 1.1.1.21 | 0.466 | |
| 2o8h | 227 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 4jq2 | SUZ | Aldo-keto reductase family 1 member C2 | / | 0.466 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.465 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.465 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2r86 | ATP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.464 | |
| 1t41 | ID5 | Aldose reductase | 1.1.1.21 | 0.463 | |
| 1gt5 | BZQ | Odorant-binding protein | / | 0.461 | |
| 3ba6 | AN2 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.461 | |
| 3szf | DCQ | Sulfide-quinone reductase | / | 0.461 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.460 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.460 | |
| 1rxj | BNI | Streptavidin | / | 0.459 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.459 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.459 | |
| 4jqa | ID8 | Aldo-keto reductase family 1 member C2 | / | 0.459 | |
| 5kf2 | ACO | Predicted acetyltransferase | / | 0.459 | |
| 1euy | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.458 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.458 | |
| 4jq3 | ZOM | Aldo-keto reductase family 1 member C2 | / | 0.458 | |
| 4zme | ADN | Myosin heavy chain kinase A | 2.7.11.7 | 0.458 | |
| 1el4 | CTZ | Obelin | / | 0.457 | |
| 3nn6 | HNK | 6-hydroxy-L-nicotine oxidase | / | 0.457 | |
| 1pj7 | FFO | Dimethylglycine oxidase | 1.5.3.10 | 0.456 | |
| 1w87 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.456 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.456 | |
| 3ght | LDT | Aldose reductase | 1.1.1.21 | 0.456 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.455 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.455 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.455 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.454 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.453 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.453 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 4ia0 | 5BB | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.453 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.453 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 5d0r | B1T | Adenylate cyclase type 10 | / | 0.453 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.452 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 2pdh | 47D | Aldose reductase | 1.1.1.21 | 0.451 | |
| 3ele | PLP | Aminotransferase | / | 0.451 | |
| 3ugr | IMN | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 1thz | 326 | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.450 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2o6h | INI | 6,7-dimethyl-8-ribityllumazine synthase 1 | 2.5.1.78 | 0.450 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.450 | |
| 3uph | 0C1 | Genome polyprotein | 2.7.7.48 | 0.450 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.450 | |
| 4jtr | IZP | Aldo-keto reductase family 1 member C2 | / | 0.450 | |
| 5dsg | 0HK | Muscarinic acetylcholine receptor M4 | / | 0.450 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.449 | |
| 1u70 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.449 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.448 | |
| 4jtr | IBP | Aldo-keto reductase family 1 member C2 | / | 0.448 | |
| 1yci | NDF | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.447 | |
| 2pdn | 47D | Aldose reductase | 1.1.1.21 | 0.447 | |
| 2xej | OKD | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.447 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3ghu | LDT | Aldose reductase | 1.1.1.21 | 0.447 | |
| 3r6i | JMS | Aldo-keto reductase family 1 member C3 | / | 0.447 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4xo7 | ASD | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.446 | |
| 2d06 | EST | Sulfotransferase 1A1 | 2.8.2.1 | 0.446 | |
| 2i16 | LDT | Aldose reductase | 1.1.1.21 | 0.446 | |
| 3hf8 | ML0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.446 | |
| 4jq1 | NPS | Aldo-keto reductase family 1 member C2 | / | 0.446 | |
| 4jtq | FLP | Aldo-keto reductase family 1 member C2 | / | 0.446 | |
| 4jxx | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.446 | |
| 4n1f | CZH | Obelin | / | 0.446 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.445 | |
| 2iki | 388 | Aldose reductase | 1.1.1.21 | 0.445 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.444 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1yun | ATP | Probable nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.444 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.444 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.444 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.444 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3c10 | TSN | Histone deacetylase 7 | 3.5.1.98 | 0.444 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.444 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4i9z | 5BA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.444 | |
| 4kfj | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4y17 | LAE | Transcriptional regulator of ftsQAZ gene cluster | / | 0.444 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.443 | |
| 2pdx | ZST | Aldose reductase | 1.1.1.21 | 0.443 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.443 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 3uwe | VJJ | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 3zns | NU7 | Histone deacetylase 7 | 3.5.1.98 | 0.443 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4b64 | NAP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4ckc | SAH | mRNA-capping enzyme catalytic subunit | 2.1.1.56 | 0.443 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 4xzj | NAD | Putative NAD(+)--arginine ADP-ribosyltransferase Vis | 2.4.2.31 | 0.443 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 2f0y | 3MN | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2pdf | ZST | Aldose reductase | 1.1.1.21 | 0.442 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 2r6k | GTX | Glutathione S-transferase A1 | 2.5.1.18 | 0.442 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.442 | |
| 4dyp | 0MS | Nucleoprotein | / | 0.442 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.442 | |
| 5a4w | QCT | Glutathione S-transferase F2 | 2.5.1.18 | 0.442 | |
| 5cto | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.442 | |
| 2vqj | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.441 | |
| 2xeg | CI9 | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.441 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.441 | |
| 4hcy | 0YN | Transketolase | / | 0.441 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.441 | |
| 4m48 | 21B | Sodium-dependent dopamine transporter | / | 0.441 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.441 | |
| 1qtq | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.440 | |
| 1qv0 | CZH | Obelin | / | 0.440 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 1xng | DND | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.440 | |
| 2d2g | DZZ | Phosphotriesterase | / | 0.440 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 3r7m | SUZ | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 3ug8 | IMN | Aldo-keto reductase family 1 member C3 | / | 0.440 | |
| 4li6 | 1XO | Tankyrase-1 | 2.4.2.30 | 0.440 | |
| 4oex | 5EO | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.440 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.440 |