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 |
|---|---|---|---|
| 3n9j | EAA | Glutathione S-transferase P | 2.5.1.18 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3n9j | EAA | Glutathione S-transferase P | 2.5.1.18 | 1.000 | |
| 3csj | CBL | Glutathione S-transferase P | 2.5.1.18 | 0.636 | |
| 1aqx | GTD | Glutathione S-transferase P | 2.5.1.18 | 0.633 | |
| 3gus | N11 | Glutathione S-transferase P | 2.5.1.18 | 0.630 | |
| 1aqv | 0HG | Glutathione S-transferase P | 2.5.1.18 | 0.619 | |
| 3dgq | EAA | Glutathione S-transferase P | 2.5.1.18 | 0.616 | |
| 2pgt | GPR | Glutathione S-transferase P | 2.5.1.18 | 0.604 | |
| 3ie3 | N11 | Glutathione S-transferase P | 2.5.1.18 | 0.576 | |
| 2a2s | GSN | Glutathione S-transferase P | 2.5.1.18 | 0.569 | |
| 13gs | SAS | Glutathione S-transferase P | 2.5.1.18 | 0.563 | |
| 3pgt | GBX | Glutathione S-transferase P | 2.5.1.18 | 0.558 | |
| 9gss | GTX | Glutathione S-transferase P | 2.5.1.18 | 0.558 | |
| 3o76 | GTB | Glutathione S-transferase P 1 | 2.5.1.18 | 0.556 | |
| 2oac | GTB | Glutathione S-transferase P 1 | 2.5.1.18 | 0.522 | |
| 2glr | GTX | Glutathione S-transferase P 1 | 2.5.1.18 | 0.521 | |
| 2oa7 | GTX | Glutathione S-transferase P 1 | 2.5.1.18 | 0.510 | |
| 2oad | GTB | Glutathione S-transferase P 1 | 2.5.1.18 | 0.509 | |
| 2xvw | 9NR | Serum albumin | / | 0.497 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.493 | |
| 4iae | 1DX | Alr2278 protein | / | 0.493 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.482 | |
| 2po3 | T4K | 4-dehydrase | / | 0.479 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.474 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.473 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.472 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.471 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.470 | |
| 3ny9 | JSZ | Beta-2 adrenergic receptor | / | 0.470 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.469 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.469 | |
| 3b9l | AZZ | Serum albumin | / | 0.468 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.466 | |
| 1wuu | ANP | Galactokinase | 2.7.1.6 | 0.464 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.464 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.464 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.463 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.460 | |
| 3c1o | NAP | Eugenol synthase | / | 0.460 | |
| 3ld6 | BCD | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.460 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.459 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.459 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.457 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.456 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.456 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.456 | |
| 2xvv | 9DN | Serum albumin | / | 0.456 | |
| 4was | COO | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.456 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.455 | |
| 4boe | CLR | Japanin | / | 0.455 | |
| 4n1g | CEI | Obelin | / | 0.455 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.455 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.454 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.453 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.453 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.453 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.453 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.453 | |
| 3p9t | TCL | Repressor | / | 0.453 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.452 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.452 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.451 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.451 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.451 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.451 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.451 | |
| 4iah | 1DX | Alr2278 protein | / | 0.451 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.450 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.449 | |
| 2bxm | IMN | Serum albumin | / | 0.449 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.449 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.449 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.449 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.449 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.449 | |
| 1mtc | GPR | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.448 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.448 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.448 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.448 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.448 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.446 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.446 | |
| 1zdw | FLV | Prenyltransferase | / | 0.446 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.446 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.446 | |
| 3att | ATP | Putative aminoglycoside phosphotransferase | 2.7.1 | 0.446 | |
| 3oia | A31 | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.445 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.445 | |
| 2r4u | ADP | Glycogen synthase | 2.4.1.21 | 0.445 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4pnr | G18 | Tankyrase-2 | 2.4.2.30 | 0.445 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.444 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.444 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.444 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.444 | |
| 3u9y | 09L | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.444 | |
| 4hr2 | ADP | Nucleoside diphosphate kinase | / | 0.444 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.443 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.442 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.442 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.442 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.442 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.442 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.441 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.441 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 2std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.441 | |
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 0.441 | |
| 3v2u | ATP | Protein GAL3 | / | 0.441 | |
| 6gsu | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.441 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.440 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.440 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.440 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.440 | |
| 4eqs | COA | Coenzyme A disulfide reductase | / | 0.440 | |
| 4mm7 | 29J | Na(+):neurotransmitter symporter (Snf family) | / | 0.440 |