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 |
|---|---|---|---|
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 | 1.000 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.696 | |
| 3pd2 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.591 | |
| 3pd3 | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.590 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.560 | |
| 3pd5 | TSB | Threonine--tRNA ligase | 6.1.1.3 | 0.558 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.555 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.554 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.548 | |
| 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 | |
| 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 | 0.477 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.477 | |
| 4dfn | 0K1 | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.472 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.471 | |
| 4mwh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.470 | |
| 3zze | 6XP | Hepatocyte growth factor receptor | 2.7.10.1 | 0.469 | |
| 4hyi | 1AO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.469 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.468 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.467 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.464 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.464 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.464 | |
| 3t7x | 4SH | Endothiapepsin | 3.4.23.22 | 0.464 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.462 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.462 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.462 | |
| 1hk1 | T44 | Serum albumin | / | 0.461 | |
| 4nbi | D3Y | D-tyrosyl-tRNA(Tyr) deacylase | / | 0.461 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.460 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 2bil | BI1 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.459 | |
| 4fi1 | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.459 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.458 | |
| 3bgq | VX2 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.458 | |
| 3she | I85 | MAP kinase-activated protein kinase 3 | 2.7.11.1 | 0.458 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.458 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.458 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.458 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.457 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.457 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 3w0n | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.456 | |
| 4jqe | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.456 | |
| 2jko | BIJ | Focal adhesion kinase 1 | 2.7.10.2 | 0.453 | |
| 3a4p | DFQ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.453 | |
| 5cvh | ADP | Casein kinase II subunit alpha | 2.7.11.1 | 0.453 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.452 | |
| 3oom | 507 | Activin receptor type-1 | 2.7.11.30 | 0.452 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.452 | |
| 4eb4 | D16 | Thymidylate synthase | 2.1.1.45 | 0.452 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 2j5s | KTA | Alr4455 protein | / | 0.451 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.451 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.450 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.449 | |
| 4bgg | 844 | Activin receptor type-1 | 2.7.11.30 | 0.449 | |
| 4dym | IYZ | Activin receptor type-1 | 2.7.11.30 | 0.449 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 1fml | RTL | Retinol dehydratase | / | 0.448 | |
| 3l9l | L9L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 4gmy | 0X5 | Tyrosine-protein kinase JAK2 | / | 0.448 | |
| 3ely | SAH | Methyltransferase | / | 0.447 | |
| 4ix6 | ADP | Uncharacterized protein | / | 0.447 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.446 | |
| 4fkq | 42K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 4lfi | GNP | Casein kinase II subunit alpha | 2.7.11.1 | 0.446 | |
| 5ikq | JMS | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.446 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 3cqu | CQU | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.445 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.445 | |
| 3l9m | L9M | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 3l9n | L9N | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 3n1s | 5GP | Purine nucleoside phosphoramidase | / | 0.445 | |
| 3r7e | X88 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.444 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.444 | |
| 4k5o | 1OT | M1 family aminopeptidase | 3.4.11 | 0.444 | |
| 4lm5 | Q17 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.444 | |
| 5hbs | RTL | Retinol-binding protein 1 | / | 0.444 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2cke | IQU | Death-associated protein kinase 2 | / | 0.443 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3pgi | F41 | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4dtk | 7LI | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.443 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.442 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.442 | |
| 1yhs | STU | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.442 | |
| 2x9f | X9F | Ephrin type-B receptor 4 | 2.7.10.1 | 0.442 | |
| 2xsz | ATP | RuvB-like 2 | 3.6.4.12 | 0.442 | |
| 3bbt | FMM | Receptor tyrosine-protein kinase erbB-4 | 2.7.10.1 | 0.442 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.442 | |
| 3prs | RIT | Endothiapepsin | 3.4.23.22 | 0.442 | |
| 3qzi | X72 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.442 | |
| 4v12 | POG | MaoC like domain protein | / | 0.442 | |
| 4xnh | ACO | N-terminal acetyltransferase A complex subunit NAT5 | 2.3.1 | 0.442 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.442 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.441 | |
| 2xj2 | 985 | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.441 | |
| 4hvi | 19S | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.441 | |
| 4ifc | ADP | Serine/threonine-protein kinase PRP4 homolog | 2.7.11.1 | 0.441 | |
| 4rrj | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.441 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.441 | |
| 1od1 | 0QS | Endothiapepsin | 3.4.23.22 | 0.440 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.440 | |
| 2ewp | TXF | Estrogen-related receptor gamma | / | 0.440 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.440 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.440 | |
| 3i4b | Z48 | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.440 | |
| 3ukr | CKH | Actin-related protein 3 | / | 0.440 | |
| 3ukr | CKH | Actin-related protein 2 | / | 0.440 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.440 | |
| 3zlo | X8U | Bcl-2-like protein 1 | / | 0.440 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.440 | |
| 4oth | DRN | Serine/threonine-protein kinase N1 | / | 0.440 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.440 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.440 |