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 |
|---|---|---|---|
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 | 1.000 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.691 | |
| 3pd5 | TSB | Threonine--tRNA ligase | 6.1.1.3 | 0.593 | |
| 3pd2 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.591 | |
| 3pd3 | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.590 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.564 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.559 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.554 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.546 | |
| 4rrh | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.530 | |
| 4rrf | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.527 | |
| 4rrm | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.527 | |
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.520 | |
| 4rrc | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.516 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.515 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.513 | |
| 4rra | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.508 | |
| 4rrl | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.506 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.500 | |
| 4rrd | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.494 | |
| 4rr9 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.489 | |
| 4rr8 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.487 | |
| 4rrb | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.484 | |
| 4rrk | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.479 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.476 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.473 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.471 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.471 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.470 | |
| 4hyi | 1AO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.469 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.468 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.468 | |
| 4mwh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.468 | |
| 3zze | 6XP | Hepatocyte growth factor receptor | 2.7.10.1 | 0.465 | |
| 4dfn | 0K1 | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.464 | |
| 3she | I85 | MAP kinase-activated protein kinase 3 | 2.7.11.1 | 0.462 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.462 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 5ajq | DB8 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.460 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.459 | |
| 3bgq | VX2 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.458 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.458 | |
| 4fi1 | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.458 | |
| 4nbi | D3Y | D-tyrosyl-tRNA(Tyr) deacylase | / | 0.458 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.458 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.456 | |
| 2bil | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.456 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.456 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.456 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.456 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.456 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.455 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.454 | |
| 3pgi | F41 | Endothiapepsin | 3.4.23.22 | 0.454 | |
| 4jqe | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.454 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 2jko | BIJ | Focal adhesion kinase 1 | 2.7.10.2 | 0.453 | |
| 3t7x | 4SH | Endothiapepsin | 3.4.23.22 | 0.453 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 3a4p | DFQ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.452 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.452 | |
| 4a4v | YFD | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 5cvh | ADP | Casein kinase II subunit alpha | 2.7.11.1 | 0.452 | |
| 3cqu | CQU | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.451 | |
| 3vf9 | 477 | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.451 | |
| 3w0n | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.451 | |
| 4xz3 | COA | Acyl-CoA synthetase (NDP forming) | / | 0.451 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.451 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 3oom | 507 | Activin receptor type-1 | 2.7.11.30 | 0.450 | |
| 4hvi | 19S | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.450 | |
| 4rel | KMP | Glycosyltransferase | / | 0.450 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.449 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 2yfe | YFE | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 3nhw | ZXZ | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.448 | |
| 5j23 | A2R | Putative 2-hydroxyacid dehydrogenase | / | 0.448 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.447 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 4gmy | 0X5 | Tyrosine-protein kinase JAK2 | / | 0.447 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.446 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.445 | |
| 3ely | SAH | Methyltransferase | / | 0.445 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.445 | |
| 3l9l | L9L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 1q4u | 4CA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.444 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 2j5s | KTA | Alr4455 protein | / | 0.444 | |
| 3r7e | X88 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.444 | |
| 4eb4 | D16 | Thymidylate synthase | 2.1.1.45 | 0.444 | |
| 4fob | 0US | ALK tyrosine kinase receptor | 2.7.10.1 | 0.444 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4lm5 | Q17 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.444 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.444 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.444 | |
| 5hbs | RTL | Retinol-binding protein 1 | / | 0.444 | |
| 1zrq | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.443 | |
| 2j9g | ANP | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3l9n | L9N | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 3mtf | A3F | Activin receptor type-1 | 2.7.11.30 | 0.443 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 1qiw | DPD | Calmodulin | / | 0.442 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.442 | |
| 1yhs | STU | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.442 | |
| 3prs | RIT | Endothiapepsin | 3.4.23.22 | 0.442 | |
| 4bdf | H3R | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.442 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.442 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 2xj2 | 985 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 3pi0 | F91 | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 3qzi | X72 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.441 | |
| 4ful | 0VU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 4rrj | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.441 | |
| 1od1 | 0QS | Endothiapepsin | 3.4.23.22 | 0.440 | |
| 1w8c | N69 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.440 | |
| 3at4 | CCK | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 3ukr | CKH | Actin-related protein 3 | / | 0.440 | |
| 3ukr | CKH | Actin-related protein 2 | / | 0.440 | |
| 3v8w | 0G2 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.440 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.440 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.440 |