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 |
|---|---|---|---|
| 2viz | VG4 | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2viz | VG4 | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 2vj7 | VG6 | Beta-secretase 1 | 3.4.23.46 | 0.775 | |
| 2vj9 | VG7 | Beta-secretase 1 | 3.4.23.46 | 0.681 | |
| 2xfi | XFI | Beta-secretase 1 | 3.4.23.46 | 0.644 | |
| 2xfk | AA9 | Beta-secretase 1 | 3.4.23.46 | 0.576 | |
| 2vnm | CM8 | Beta-secretase 1 | 3.4.23.46 | 0.562 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.540 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.538 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.537 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.512 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.508 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.488 | |
| 4blr | UTP | NTPase P4 | / | 0.487 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.484 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.483 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.478 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.475 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.473 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.466 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.465 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.465 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.461 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.458 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.458 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.457 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.456 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.456 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.455 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.454 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.453 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.453 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.452 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.452 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.449 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.449 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.449 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.448 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.448 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.448 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.447 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.446 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.446 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.446 | |
| 3pwm | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.445 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.445 | |
| 2p3b | 3TL | V-1 protease | / | 0.445 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.445 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.445 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.445 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.445 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.443 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.442 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 3tog | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.442 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.442 | |
| 1bmf | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.441 | |
| 1bmf | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.441 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.441 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3pmy | 41L | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4nau | AGS | Phosphopantetheine adenylyltransferase | / | 0.441 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.440 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 1m0b | 0ZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.440 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.440 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.440 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.440 |