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 |
|---|---|---|---|
| 2d52 | COA | 5,7-dihydroxy-2-methylchromone synthase | 2.3.1.216 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2d52 | COA | 5,7-dihydroxy-2-methylchromone synthase | 2.3.1.216 | 1.000 | |
| 2d3m | COA | 5,7-dihydroxy-2-methylchromone synthase | 2.3.1.216 | 0.794 | |
| 1ee0 | CAA | 2-pyrone synthase | / | 0.614 | |
| 3wxy | COA | Uncharacterized protein | / | 0.522 | |
| 3wd7 | COA | Acridone synthase | / | 0.497 | |
| 4jaq | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.492 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.473 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.471 | |
| 3ics | ADP | Coenzyme A disulfide reductase | / | 0.471 | |
| 3stx | BKA | Methylketone synthase I | / | 0.470 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.469 | |
| 4jd3 | COA | Alpha-pyrone synthesis polyketide synthase-like Pks11 | 2.3.1 | 0.466 | |
| 1ie4 | T44 | Transthyretin | / | 0.465 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1bq6 | COA | Chalcone synthase 2 | 2.3.1.74 | 0.462 | |
| 1ffu | FAD | Carbon monoxide dehydrogenase medium chain | / | 0.461 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.461 | |
| 4h4q | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.461 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.460 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2q70 | DC8 | Estrogen receptor | / | 0.460 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.460 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.460 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.459 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.458 | |
| 1sn5 | T3 | Transthyretin | / | 0.457 | |
| 4h3c | 0YZ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.457 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.456 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.455 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.455 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.454 | |
| 4ejg | NCT | Cytochrome P450 2A13 | 1.14.14.1 | 0.454 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.454 | |
| 2hqp | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 4hgl | 0YO | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.453 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.452 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.452 | |
| 4aw3 | MYV | Mycinamicin IV hydroxylase/epoxidase | / | 0.452 | |
| 4ma6 | 28E | Ara h 8 allergen | / | 0.452 | |
| 4z69 | DIF | Serum albumin | / | 0.452 | |
| 2bxm | IMN | Serum albumin | / | 0.451 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.451 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.451 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.450 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.450 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 3q8x | UD1 | Toxin zeta | / | 0.450 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.450 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.449 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.449 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.449 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.449 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.449 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 3el8 | PD5 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.448 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.448 | |
| 4hee | 14R | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.446 | |
| 3cgf | JNF | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.446 | |
| 3v8w | 0G2 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.446 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.446 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.446 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.446 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.446 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.446 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.445 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.444 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.444 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.444 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.444 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.444 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.444 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.444 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.444 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1q4u | 4CA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.443 | |
| 1uum | AFI | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.443 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.443 | |
| 2p4y | C03 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.443 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.443 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1fpq | SAM | Isoliquiritigenin 2'-O-methyltransferase | / | 0.442 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2y3s | TIR | TamL | / | 0.442 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 4feq | 0T8 | Tyrosine-protein kinase receptor TYRO3 | 2.7.10.1 | 0.442 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.442 | |
| 4jlc | SU6 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.442 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.441 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.441 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.441 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.441 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.441 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.440 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.440 | |
| 1q4g | BFL | Prostaglandin G/H synthase 1 | 1.14.99.1 | 0.440 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 2g0n | GDP | Ras-related C3 botulinum toxin substrate 3 | / | 0.440 | |
| 2hk5 | 1BM | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.440 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 3dpd | 41A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.440 | |
| 3okx | SAM | S-adenosyl-L-methionine-binding protein RPA0152 | / | 0.440 | |
| 3pvr | BYC | 1,2-phenylacetyl-CoA epoxidase, subunit A | 1.14.13.149 | 0.440 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.440 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.440 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.440 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.440 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.440 |