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 |
|---|---|---|---|
| 1k6m | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 | 2.7.1.105 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1k6m | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 | 2.7.1.105 | 1.000 | |
| 3qpv | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.653 | |
| 1bif | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.652 | |
| 2i1v | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.652 | |
| 4ma4 | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.613 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.607 | |
| 2axn | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | / | 0.591 | |
| 2bif | ANP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.591 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.484 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.482 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.473 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 1r2j | FAD | FkbI | / | 0.472 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.472 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.472 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.470 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.470 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.469 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.469 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.469 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.468 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.468 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.468 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.466 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.465 | |
| 4h3y | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.465 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.463 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.463 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.463 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 2hfp | NSI | Peroxisome proliferator-activated receptor gamma | / | 0.462 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.462 | |
| 3rnn | RNN | Glutamate receptor 2 | / | 0.462 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.462 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.461 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.460 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.459 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.459 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.459 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.458 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.458 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.458 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.458 | |
| 1eh4 | IC1 | Casein kinase I homolog 1 | 2.7.11.1 | 0.457 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.457 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.456 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.455 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.455 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.454 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.454 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.454 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.453 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.453 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.453 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.453 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.452 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.452 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.452 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.452 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.451 | |
| 3be9 | P04 | Casein kinase II subunit alpha | 2.7.11.1 | 0.451 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.451 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.451 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.451 | |
| 4oj4 | DIF | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.451 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.451 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.450 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.450 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.450 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.450 | |
| 4l8u | 9AZ | Serum albumin | / | 0.450 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.450 | |
| 5bmv | VLB | Tubulin alpha-1B chain | / | 0.450 | |
| 5bmv | VLB | Tubulin beta chain | / | 0.450 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.449 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.449 | |
| 4alh | A9P | Bromodomain-containing protein 2 | / | 0.449 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.448 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.448 | |
| 1e7a | PFL | Serum albumin | / | 0.448 | |
| 1hii | C20 | Gag-Pol polyprotein | / | 0.448 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.448 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.448 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.448 | |
| 4irn | FAD | AnaB | / | 0.448 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.448 | |
| 4nr4 | 2LK | CREB-binding protein | / | 0.448 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.448 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.447 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.447 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.447 | |
| 2brb | PFQ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.447 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2vwc | BC2 | ATP-dependent molecular chaperone HSP82 | / | 0.447 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.447 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.447 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.447 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.447 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.446 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.446 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.446 | |
| 3qlf | PD5 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.446 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.446 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.446 | |
| 4bqh | 9VU | UDP-N-acetylglucosamine pyrophosphorylase, putative | / | 0.446 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.445 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.445 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.445 | |
| 3bhe | BZN | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.445 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.445 | |
| 4eh3 | NAR | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 4okt | 198 | Androgen receptor | / | 0.445 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.445 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1rbm | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.444 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.444 | |
| 2h8h | H8H | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.444 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.444 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.444 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.444 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.444 | |
| 3oct | 1N1 | Tyrosine-protein kinase BTK | 2.7.10.2 | 0.444 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.444 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4akn | S5B | Bromodomain-containing protein 2 | / | 0.444 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.444 | |
| 4ix5 | ANP | Uncharacterized protein | / | 0.444 | |
| 4lj5 | ADP | Chaperone protein ClpB | / | 0.444 | |
| 4nxw | ADP | Mitochondrial dynamics protein MID51 | / | 0.444 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.443 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2daa | DCS | D-alanine aminotransferase | 2.6.1.21 | 0.443 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.443 | |
| 2wpx | ACO | Orf14 | / | 0.443 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.443 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.443 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.442 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.442 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.442 | |
| 2hj3 | FAD | FAD-linked sulfhydryl oxidase ERV1 | / | 0.442 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3lu8 | IQX | Serum albumin | / | 0.442 | |
| 3t11 | 3T1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.442 | |
| 4a4v | YFD | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.442 | |
| 1qmf | KEF | Penicillin-binding protein 2x | / | 0.441 | |
| 2jlc | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.441 | |
| 2q61 | SF1 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2ya3 | J7V | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.441 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.441 | |
| 3n87 | N87 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.441 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.441 | |
| 3v3m | 0EN | Replicase polyprotein 1a | 3.4.19.12 | 0.441 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.441 | |
| 3zux | TCH | Transporter | / | 0.441 | |
| 4fod | 0UV | ALK tyrosine kinase receptor | 2.7.10.1 | 0.441 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 4j3i | 1K0 | Bromodomain-containing protein 4 | / | 0.441 | |
| 4l9k | EHF | Serum albumin | / | 0.441 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.441 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1g28 | FMN | PHY3 | / | 0.440 | |
| 1hxb | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1pp9 | SMA | Cytochrome b | / | 0.440 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.440 | |
| 2e20 | B4P | Propionate kinase | / | 0.440 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.440 | |
| 2pnu | ENM | Androgen receptor | / | 0.440 | |
| 3ef6 | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.440 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.440 | |
| 3kgc | LY7 | Glutamate receptor 2 | / | 0.440 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.440 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.440 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4as9 | 4QS | ATP-dependent molecular chaperone HSP82 | / | 0.440 | |
| 4aw3 | MYV | Mycinamicin IV hydroxylase/epoxidase | / | 0.440 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4gmy | 0X5 | Tyrosine-protein kinase JAK2 | / | 0.440 | |
| 4im0 | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.440 | |
| 4wkq | IRE | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 |