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 |
|---|---|---|---|
| 3cmp | EB4 | Neutrophil gelatinase-associated lipocalin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3cmp | EB4 | Neutrophil gelatinase-associated lipocalin | / | 1.000 | |
| 1ryw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.505 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.497 | |
| 2cah | NDP | Catalase | 1.11.1.6 | 0.495 | |
| 2xpv | MIY | Tetracycline repressor protein class D | / | 0.495 | |
| 1szc | CNA | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.491 | |
| 2wd4 | TBV | Ascorbate peroxidase | / | 0.490 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.489 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.483 | |
| 4nwi | CTN | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.482 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 3kqj | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.480 | |
| 3swq | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.478 | |
| 4gtv | 7TR | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.475 | |
| 4biz | ADP | Sensor histidine kinase CpxA | / | 0.474 | |
| 3iss | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.473 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.473 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.473 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.472 | |
| 4en4 | ATP | Pyridoxal kinase | 2.7.1.35 | 0.472 | |
| 2imk | GTX | AGAP009194-PA | / | 0.471 | |
| 3v4t | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.470 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.469 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.468 | |
| 2cdu | FAD | NADH oxidase | / | 0.467 | |
| 2r6j | NDP | Eugenol synthase 1 | 1.1.1.318 | 0.467 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.467 | |
| 3lpf | Z77 | Beta-glucuronidase | 3.2.1.31 | 0.466 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.465 | |
| 1equ | EQI | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.465 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 3gnw | XNC | Genome polyprotein | 2.7.7.48 | 0.464 | |
| 1xmm | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.463 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.463 | |
| 4uz6 | SCR | Palmitoleoyl-protein carboxylesterase NOTUM | / | 0.463 | |
| 2x86 | ADP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.462 | |
| 1i2c | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.461 | |
| 1st0 | GTG | m7GpppX diphosphatase | 3.6.1.59 | 0.461 | |
| 3gol | XND | Genome polyprotein | 2.7.7.48 | 0.461 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.461 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.460 | |
| 3hpq | AP5 | Adenylate kinase | / | 0.460 | |
| 3qcj | NX4 | Receptor-type tyrosine-protein phosphatase gamma | 3.1.3.48 | 0.460 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.459 | |
| 3cmp | DBH | Neutrophil gelatinase-associated lipocalin | / | 0.459 | |
| 4a6e | ASE | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.459 | |
| 1n5t | OAL | ActVA 6 protein | / | 0.458 | |
| 4fdp | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.458 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.458 | |
| 1f3p | FAD | Ferredoxin reductase | / | 0.456 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2gn4 | UD1 | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.456 | |
| 2mjp | ANP | dITP/XTP pyrophosphatase | 3.6.1.19 | 0.456 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.456 | |
| 4xr9 | TMP | CalS8 | / | 0.456 | |
| 5aqz | SGV | Heat shock 70 kDa protein 1A | / | 0.456 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.455 | |
| 3upi | 0C2 | Genome polyprotein | 2.7.7.48 | 0.455 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.454 | |
| 3fzf | ATP | Heat shock cognate 71 kDa protein | / | 0.454 | |
| 4bqy | FNT | Egl nine homolog 1 | / | 0.454 | |
| 4iqk | IQK | Kelch-like ECH-associated protein 1 | / | 0.454 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2e20 | B4P | Propionate kinase | / | 0.453 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.453 | |
| 1ja1 | NAP | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 1w29 | TS0 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 2bn4 | NAP | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.452 | |
| 3hv4 | L51 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 3od4 | 8XQ | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.452 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.452 | |
| 4at4 | T6E | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.452 | |
| 4bkj | STI | Epithelial discoidin domain-containing receptor 1 | 2.7.10.1 | 0.452 | |
| 4dym | IYZ | Activin receptor type-1 | 2.7.11.30 | 0.452 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.452 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3ebl | GA4 | Gibberellin receptor GID1 | / | 0.451 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.451 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4r7u | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.451 | |
| 1rvv | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2bue | COA | AAC(6')-Ib | / | 0.450 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3cvy | FAD | RE11660p | / | 0.450 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.450 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.449 | |
| 2rl1 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.448 | |
| 3koq | FMN | Putative nitroreductase | / | 0.448 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.448 | |
| 4jem | C5P | CMP/hydroxymethyl CMP hydrolase | / | 0.448 | |
| 4k97 | ATP | Cyclic GMP-AMP synthase | / | 0.448 | |
| 4lis | UPG | UDP-glucose 4-epimerase (Eurofung) | / | 0.448 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.447 | |
| 1u1c | BAU | Uridine phosphorylase | 2.4.2.3 | 0.447 | |
| 2a19 | ANP | Interferon-induced, double-stranded RNA-activated protein kinase | 2.7.11.1 | 0.447 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.447 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.447 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 1osv | CHC | Bile acid receptor | / | 0.446 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.446 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.446 | |
| 3af4 | GCP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3nf8 | CDQ | Gag-Pol polyprotein | / | 0.446 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4g0k | 0VS | Glutathionyl-hydroquinone reductase YqjG | 1.8 | 0.446 | |
| 4xeo | A5A | Alanine--tRNA ligase, cytoplasmic | / | 0.446 | |
| 1l2o | ADP | Myosin heavy chain, striated muscle | / | 0.445 | |
| 1zzq | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.445 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 2xau | ADP | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | 3.6.4.13 | 0.445 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.445 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.445 | |
| 3e6o | H4B | Nitric oxide synthase, inducible | 1.14.13.39 | 0.445 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.445 | |
| 3t99 | ADP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.445 | |
| 3x0c | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.445 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.445 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 2wq7 | FAD | RE11660p | / | 0.444 | |
| 3lth | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.444 | |
| 3n5v | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 4lv5 | ADP | Rhoptry protein 5B | / | 0.444 | |
| 4zm3 | PLP | Aminotransferase | / | 0.444 | |
| 5fko | TDC | Tetracycline repressor protein class D | / | 0.444 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 1ses | AHX | Serine--tRNA ligase | 6.1.1.11 | 0.443 | |
| 2j7t | 274 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.443 | |
| 3lpg | Z78 | Beta-glucuronidase | 3.2.1.31 | 0.443 | |
| 4bva | T3 | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.443 | |
| 4gqe | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.443 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.443 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.442 | |
| 3ske | 054 | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 4cqn | ILA | Leucine--tRNA ligase | / | 0.442 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.442 | |
| 5cto | NTD | 4-hydroxyphenylpyruvate dioxygenase | 1.13.11.27 | 0.442 | |
| 1uoo | GLY_PHE_ARG_PRO | Prolyl endopeptidase | 3.4.21.26 | 0.441 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 3ge6 | FMN | Nitroreductase | / | 0.441 | |
| 3jt7 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 3jt8 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 3kp0 | Z98 | D-ornithine 4,5-aminomutase subunit beta | / | 0.441 | |
| 3mzh | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.441 | |
| 3rv6 | VAE | Salicylate synthase | / | 0.441 | |
| 3ska | 053 | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 4eux | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 4yp1 | 2BA | Stimulator of interferon genes protein | / | 0.441 | |
| 5bv3 | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.441 | |
| 5iw4 | NAD | NADH pyrophosphatase | / | 0.441 | |
| 1mdl | RMN | Mandelate racemase | / | 0.440 | |
| 1r8q | AFB | Cytohesin-2 | / | 0.440 | |
| 1r8q | AFB | ADP-ribosylation factor 1 | / | 0.440 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3eej | 53R | Uncharacterized protein | / | 0.440 | |
| 3rha | FDA | Putrescine oxidase | / | 0.440 | |
| 3wdl | ATP | 4-phosphopantoate--beta-alanine ligase | 6.3.2.36 | 0.440 | |
| 4fw0 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 4ie6 | UN9 | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.440 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 |