sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2onf | COA | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2onf | COA | Uncharacterized protein | / | 1.000 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.499 | |
| 2c6c | 24I | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.496 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.493 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.481 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.476 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.471 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.468 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 2xeg | CI9 | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.464 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.464 | |
| 3gy9 | COA | GCN5-related N-acetyltransferase | / | 0.462 | |
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.460 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.460 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.460 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.459 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.459 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.459 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.457 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.456 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.456 | |
| 1zdw | FLV | Prenyltransferase | / | 0.455 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.455 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1qs2 | NAD | Vip2Ac | / | 0.454 | |
| 2qmz | LDP | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.454 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.454 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.454 | |
| 4h0v | NAD | Iota toxin component Ia | / | 0.454 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.454 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.452 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.452 | |
| 2hzq | STR | Apolipoprotein D | / | 0.452 | |
| 3gya | COA | GCN5-related N-acetyltransferase | / | 0.452 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.452 | |
| 4d2d | ALA_ALA_ALA | Di-or tripeptide:H+ symporter | / | 0.452 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.452 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.452 | |
| 1lke | DOG | Bilin-binding protein | / | 0.451 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.451 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.449 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.449 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.449 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 4ykl | GMP | Aprataxin-like protein | 3 | 0.449 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.448 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.447 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.447 | |
| 2pdl | TOL | Aldose reductase | 1.1.1.21 | 0.447 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.447 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.446 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.446 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.445 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.445 | |
| 4kxj | P34 | Nucleoprotein | / | 0.445 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.445 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2vrj | NCW | Beta-glucosidase A | 3.2.1.21 | 0.443 | |
| 4nhy | PD2 | Prolyl 3-hydroxylase OGFOD1 | 1.14.11 | 0.443 | |
| 1lgt | BP3 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.442 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.442 | |
| 2r5n | TPP | Transketolase 1 | / | 0.442 | |
| 2r96 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.442 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.442 | |
| 5cuq | NSC | Genome polyprotein | / | 0.442 | |
| 1ddt | APU | Diphtheria toxin | / | 0.441 | |
| 1jf0 | CZH | Obelin | / | 0.441 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.441 | |
| 3e33 | ED7 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 3sfx | JAN | Uncharacterized protein | / | 0.441 | |
| 3v97 | SAH | Ribosomal RNA large subunit methyltransferase K/L | 2.1.1.173 | 0.441 | |
| 4j7h | TRH | PCZA361.3 | / | 0.441 | |
| 4lng | JAN | CaaX farnesyltransferase beta subunit Ram1 | / | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 3ix4 | TX1 | Transcriptional activator protein LasR | / | 0.440 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.440 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.440 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.440 | |
| 5tgz | FMN | Cannabinoid receptor 1 | / | 0.440 |