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 |
|---|---|---|---|
| 3l0l | HC3 | Nuclear receptor ROR-gamma |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 1.000 | |
| 3kyt | HC2 | Nuclear receptor ROR-gamma | / | 0.627 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.618 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.564 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.553 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.548 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.509 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.490 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.487 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.484 | |
| 4l9q | 9TP | Serum albumin | / | 0.484 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.483 | |
| 3zuy | TCH | Transporter | / | 0.483 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.482 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.482 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.479 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.479 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.479 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.479 | |
| 3p6p | A6B | Camphor 5-monooxygenase | 1.14.15.1 | 0.477 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.476 | |
| 3zux | TCH | Transporter | / | 0.476 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.476 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.475 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.474 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.474 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.473 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.473 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.472 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.471 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.471 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.470 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.470 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.470 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.470 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.469 | |
| 1rf9 | DBR | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.468 | |
| 2w4q | CBW | Prostaglandin reductase 2 | 1.3.1.48 | 0.467 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.466 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.465 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.465 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.464 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.463 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.463 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.463 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.463 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.463 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.462 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.462 | |
| 3e5a | VX6 | Aurora kinase A | 2.7.11.1 | 0.462 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.462 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.461 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.461 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.461 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.460 | |
| 4l8u | 9AZ | Serum albumin | / | 0.460 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.459 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1ci7 | CB3 | Thymidylate synthase | 2.1.1.45 | 0.458 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.458 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.458 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.458 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.457 | |
| 2jfz | 003 | Glutamate racemase | / | 0.457 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.457 | |
| 5ifi | PRX | Acetyl-coenzyme A synthetase | / | 0.457 | |
| 1osv | CHC | Bile acid receptor | / | 0.456 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.456 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.456 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.455 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.455 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.455 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.455 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.454 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.454 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.454 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.454 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.454 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.453 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.453 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.453 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.453 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.453 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.453 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.452 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.452 | |
| 3inm | NDP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.452 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.452 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.452 | |
| 5a3b | APR | SIR2 family protein | / | 0.452 | |
| 1fml | RTL | Retinol dehydratase | / | 0.451 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.451 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.451 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.451 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.451 | |
| 4d0l | 093 | Phosphatidylinositol 4-kinase beta | 2.7.1.67 | 0.451 | |
| 4elh | 53I | Dihydrofolate reductase | / | 0.451 | |
| 1olm | VTQ | SEC14-like protein 2 | / | 0.450 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.450 | |
| 3lu8 | IQX | Serum albumin | / | 0.450 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3up3 | XCA | aceDAF-12 | / | 0.450 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.450 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.450 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.449 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.449 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.449 | |
| 4fv1 | EK4 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.449 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.448 | |
| 3aba | FLI | Cytochrome P450 | / | 0.448 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.448 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.448 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.447 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.447 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.447 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.447 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.446 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.446 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.446 | |
| 4cdm | FAD | Deoxyribodipyrimidine photolyase | / | 0.446 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.446 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.446 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.445 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.445 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.445 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.445 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.445 | |
| 4kwi | 1TJ | Reductase homolog | / | 0.445 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.444 | |
| 2e9c | B75 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.444 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.444 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 4ach | KDI | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.444 | |
| 4aot | GW8 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.444 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.444 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.443 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.443 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.443 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.443 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.443 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.443 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.443 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.443 | |
| 4l9k | EHF | Serum albumin | / | 0.443 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.443 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.442 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.442 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.441 | |
| 1ju6 | LYA | Thymidylate synthase | 2.1.1.45 | 0.441 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.441 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.441 | |
| 3bhr | THG | Thymidylate synthase | / | 0.441 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.441 | |
| 3fl8 | RAR | Dihydrofolate reductase | / | 0.441 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.441 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.441 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.440 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.440 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1j4j | ACO | Acetyltransferase | 2.3.1 | 0.440 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2c7g | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.440 | |
| 2jdv | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.440 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.440 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.440 | |
| 4g6h | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.440 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.440 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.440 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.440 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.440 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 |