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 |
|---|---|---|---|
| 2uyi | ADP | Kinesin-like protein KIF11 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2uyi | ADP | Kinesin-like protein KIF11 | / | 1.000 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.505 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.495 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.486 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.486 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.483 | |
| 1eag | A70 | Candidapepsin-2 | 3.4.23.24 | 0.478 | |
| 3uu1 | 14B | Anthranilate phosphoribosyltransferase | / | 0.477 | |
| 3spt | UD1 | Bifunctional protein GlmU | / | 0.474 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.473 | |
| 4b3a | TAC | Tetracycline repressor protein class D | / | 0.473 | |
| 4y8v | ADP | Acyl-CoA synthetase (NDP forming) | / | 0.473 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.471 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.471 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.471 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.471 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.470 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.469 | |
| 3c4v | LIP | D-inositol 3-phosphate glycosyltransferase | 2.4.1.250 | 0.468 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.468 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.467 | |
| 4jxr | ACO | Acetyltransferase | / | 0.466 | |
| 4bri | UNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.465 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.464 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.464 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.463 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.462 | |
| 1lol | XMP | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.461 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.461 | |
| 4uz6 | SCR | Palmitoleoyl-protein carboxylesterase NOTUM | / | 0.461 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.460 | |
| 4hyv | PEP | Pyruvate kinase 1 | 2.7.1.40 | 0.460 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.459 | |
| 2dpx | GDP | GTP-binding protein RAD | / | 0.459 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.459 | |
| 4pao | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.459 | |
| 2zdy | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.458 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.458 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.458 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.457 | |
| 4anw | O92 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 4fry | NAD | Putative signal-transduction protein with CBS domains | / | 0.457 | |
| 4zca | ADP | Kinesin-like protein KIF11 | / | 0.457 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.456 | |
| 3cly | ACP | Fibroblast growth factor receptor 2 | / | 0.456 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.456 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.456 | |
| 4rx6 | ATP | Nitrogen regulatory PII-like protein | / | 0.456 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.455 | |
| 2oor | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.455 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.454 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.454 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2ax4 | ADP | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 | 2.7.1.25 | 0.454 | |
| 4gnc | ASO | Regucalcin | 3.1.1.17 | 0.454 | |
| 4z36 | ON3 | Lysophosphatidic acid receptor 1 | / | 0.454 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.453 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.453 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.453 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.453 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 2yqj | UD1 | UDP-N-acetylglucosamine pyrophosphorylase | 2.7.7.23 | 0.453 | |
| 3dj4 | UD1 | Bifunctional protein GlmU | / | 0.453 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.453 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.452 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.452 | |
| 4en4 | ATP | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.452 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4qxr | 1YE | Stimulator of interferon genes protein | / | 0.452 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.451 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.451 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.450 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.450 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.450 | |
| 3nmn | PYV | Abscisic acid receptor PYL1 | / | 0.450 | |
| 3o15 | 3NM | Thiamine-phosphate synthase | / | 0.450 | |
| 1ei1 | ANP | DNA gyrase subunit B | / | 0.449 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.449 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.449 | |
| 3ftq | GNP | Septin-2 | / | 0.449 | |
| 3hgm | ATP | TRAP-T-associated universal stress protein TeaD | / | 0.449 | |
| 1jed | ADP | Sulfate adenylyltransferase | / | 0.448 | |
| 2r0c | FAD | Putative FAD-monooxygenase | / | 0.448 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.448 | |
| 4azm | T4B | Fatty acid-binding protein, epidermal | / | 0.448 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.448 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.447 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.447 | |
| 2pb2 | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.447 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.447 | |
| 3epo | MP5 | Phosphomethylpyrimidine synthase | / | 0.447 | |
| 3mx5 | UTP | Nucleoprotein | / | 0.447 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.447 | |
| 4l6g | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.447 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.447 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.446 | |
| 1rdw | LAR | Actin, alpha skeletal muscle | / | 0.446 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 5bv3 | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.446 | |
| 1o01 | NAD | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.445 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.445 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.445 | |
| 3ea0 | ATP | ATPase, ParA family | / | 0.445 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.445 | |
| 3peh | IBD | Endoplasmin homolog, putative | / | 0.445 | |
| 3umo | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.445 | |
| 4a61 | ANP | Plasmid segregation protein ParM | / | 0.445 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.445 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.444 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.444 | |
| 3wb2 | YGP | Uncharacterized protein MJ0488 | / | 0.444 | |
| 4coj | DTP | Uncharacterized protein | / | 0.444 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.444 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.444 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.443 | |
| 1p9w | ANP | Type II secretion system protein E | / | 0.443 | |
| 1qy8 | RDI | Endoplasmin | / | 0.443 | |
| 1w48 | APC | NTPase P4 | / | 0.443 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.443 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.443 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.443 | |
| 4eht | ADP | 2-hydroxyisocaproyl-CoA dehydratase activator | / | 0.443 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.442 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.442 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.442 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.442 | |
| 4eiq | KCT | Putative FAD-monooxygenase | / | 0.442 | |
| 4k81 | GTP | GTPase HRas | / | 0.442 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.441 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.441 | |
| 1jdv | ADN | Purine nucleoside phosphorylase | / | 0.441 | |
| 2ad5 | ADP | CTP synthase | / | 0.441 | |
| 2bpo | NAP | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 2i5b | ADP | Pyridoxine kinase | / | 0.441 | |
| 2vax | CSC | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.441 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.441 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.441 | |
| 3cop | ADP | Glycogen synthase | 2.4.1.21 | 0.441 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.441 | |
| 3r1r | ATP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.441 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.441 | |
| 4o67 | 1SY | Cyclic GMP-AMP synthase | / | 0.441 | |
| 4xgx | ADP | FAD:protein FMN transferase | / | 0.441 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.440 | |
| 1jm6 | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.440 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.440 | |
| 2y6o | 1N1 | Ephrin type-A receptor 4 | 2.7.10.1 | 0.440 | |
| 3e8x | NAP | BH1520 protein | / | 0.440 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.440 | |
| 3op5 | REB | Serine/threonine-protein kinase VRK1 | 2.7.11.1 | 0.440 | |
| 4ge5 | A89 | Tyrosine-protein phosphatase non-receptor type 9 | 3.1.3.48 | 0.440 | |
| 4z0g | 5GP | Inosine-5'-monophosphate dehydrogenase | / | 0.440 |