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 |
|---|---|---|---|
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 1.000 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.602 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.591 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.540 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.537 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.533 | |
| 1suo | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.528 | |
| 4ejg | NCT | Cytochrome P450 2A13 | 1.14.14.1 | 0.528 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.527 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.527 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.518 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.511 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.507 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.504 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.504 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.498 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.496 | |
| 4k9v | 6AW | Cytochrome P450 3A4 | / | 0.495 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.493 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.493 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.492 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.490 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.489 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.489 | |
| 4lht | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.488 | |
| 2w0b | CMW | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.487 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.483 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.482 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.481 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.480 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.480 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.480 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.479 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.478 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.477 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.476 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.476 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.476 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.476 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.475 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.474 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.473 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.472 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.470 | |
| 4l6g | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.468 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.467 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.466 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.465 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.464 | |
| 3tjs | D0R | Cytochrome P450 3A4 | / | 0.464 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.463 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.463 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.463 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 3eej | 53R | Uncharacterized protein | / | 0.462 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.462 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.461 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.461 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.460 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.459 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 2zui | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.458 | |
| 4c9o | CAM | Cytochrome P450 | / | 0.458 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.458 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.457 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.457 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.456 | |
| 1fml | RTL | Retinol dehydratase | / | 0.456 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 4egn | TWO | Cytochrome P450 | / | 0.456 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 3zbn | COA | 3-ketoacyl-CoA thiolase-like protein | / | 0.455 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 2bxo | OPB | Serum albumin | / | 0.454 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.454 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.454 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.453 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.453 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.453 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.452 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.450 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.450 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.450 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.450 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.449 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 1t2b | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.448 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.448 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.448 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.448 | |
| 3ua1 | 08Y | Cytochrome P450 3A4 | / | 0.448 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.447 | |
| 4iah | 1DX | Alr2278 protein | / | 0.447 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.446 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.446 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.446 | |
| 1ee9 | NAD | Methylenetetrahydrofolate dehydrogenase [NAD(+)] | 1.5.1.15 | 0.445 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.445 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 2qbn | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2qw0 | 34Z | 4-chlorobenzoyl CoA ligase | / | 0.444 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.443 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.443 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.442 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.442 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.442 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.442 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.441 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.441 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.441 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 2ibz | UQ6 | Cytochrome b | / | 0.440 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.440 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 3eem | 53V | Uncharacterized protein | / | 0.440 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.440 |