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 |
|---|---|---|---|
| 3gww | SFX | Na(+):neurotransmitter symporter (Snf family) |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3gww | SFX | Na(+):neurotransmitter symporter (Snf family) | / | 1.000 | |
| 2qju | DSM | Na(+):neurotransmitter symporter (Snf family) | / | 0.649 | |
| 2q72 | IXX | Na(+):neurotransmitter symporter (Snf family) | / | 0.645 | |
| 3gwu | SRE | Na(+):neurotransmitter symporter (Snf family) | / | 0.619 | |
| 2qei | CXX | Na(+):neurotransmitter symporter (Snf family) | / | 0.564 | |
| 2q6h | CXX | Na(+):neurotransmitter symporter (Snf family) | / | 0.522 | |
| 2ayr | L4G | Estrogen receptor | / | 0.500 | |
| 2yoh | WMJ | Thymidylate kinase | / | 0.489 | |
| 1y56 | FMN | Uncharacterized protein | / | 0.488 | |
| 1y56 | FMN | 382aa long hypothetical sarcosine oxidase | / | 0.488 | |
| 3lp2 | LP9 | Gag-Pol polyprotein | 2.7.7.49 | 0.487 | |
| 4kbn | 25U | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 2w5b | AGS | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.484 | |
| 4ivq | I43 | Thymidine kinase | / | 0.479 | |
| 2i0v | 6C3 | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.477 | |
| 3n0y | APC | Adenylate cyclase 2 | / | 0.477 | |
| 3m50 | EBT | 14-3-3-like protein C | / | 0.475 | |
| 3m50 | EBT | Plasma membrane ATPase | / | 0.475 | |
| 1iah | ADP | Transient receptor potential cation channel subfamily M member 7 | 2.7.11.1 | 0.474 | |
| 4man | 1Y1 | Apoptosis regulator Bcl-2 | / | 0.474 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 2jav | 5Z5 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.469 | |
| 3nmv | PYV | Abscisic acid receptor PYL2 | / | 0.469 | |
| 2qqf | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.468 | |
| 4k9y | K9Y | Focal adhesion kinase 1 | 2.7.10.2 | 0.468 | |
| 3ov4 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.466 | |
| 4el9 | AFE | Ribosomal protein S6 kinase alpha-3 | 2.7.11.1 | 0.466 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.465 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.465 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.465 | |
| 1szc | CNA | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.464 | |
| 3rs0 | GNP | GTPase HRas | / | 0.464 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.464 | |
| 1tkz | H16 | Gag-Pol polyprotein | 2.7.7.49 | 0.463 | |
| 3lla | ACP | Myosin heavy chain kinase A | 2.7.11.7 | 0.463 | |
| 4kd7 | 9DR | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4lxd | 1XV | Apoptosis regulator Bcl-2 | / | 0.463 | |
| 4zs4 | ATP | Myosin heavy chain kinase A | 2.7.11.7 | 0.463 | |
| 1cq7 | PY5 | Aspartate aminotransferase | 2.6.1.1 | 0.462 | |
| 1fr8 | GDU | Beta-1,4-galactosyltransferase 1 | / | 0.462 | |
| 2zoz | ET | Transcriptional regulator | / | 0.462 | |
| 2ama | DHT | Androgen receptor | / | 0.461 | |
| 2xnm | WGZ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.461 | |
| 3jpv | 1DR | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.460 | |
| 4jbx | SK7 | Thymidine kinase | / | 0.459 | |
| 1jjt | BDS | Beta-lactamase | / | 0.458 | |
| 2ati | IHU | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.458 | |
| 2e1z | B4P | Propionate kinase | / | 0.458 | |
| 2q3e | UPG | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.458 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.458 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.458 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.458 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 3m8c | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.457 | |
| 4f1m | ACP | Probable serine/threonine-protein kinase roco4 | 2.7.11.1 | 0.457 | |
| 1w2c | ANP | Inositol-trisphosphate 3-kinase A | 2.7.1.127 | 0.456 | |
| 4dlz | GNP | GTPase HRas | / | 0.456 | |
| 4ds8 | A8S | Abscisic acid receptor PYL3 | / | 0.456 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.456 | |
| 1e2j | THM | Thymidine kinase | / | 0.455 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2xk8 | 5R1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.455 | |
| 3fko | FKO | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 3ka7 | FAD | Putative oxidoreductase | / | 0.455 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.454 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 3nef | PYV | Abscisic acid receptor PYL1 | / | 0.454 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.454 | |
| 4ivr | N50 | Thymidine kinase | / | 0.454 | |
| 1w78 | PD8 | Dihydrofolate synthase/folylpolyglutamate synthase | 6.3.2.12 | 0.453 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.453 | |
| 2puu | G2G | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.453 | |
| 3x0a | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.453 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.453 | |
| 4hw7 | 64M | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.453 | |
| 4kak | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1ia9 | ANP | Transient receptor potential cation channel subfamily M member 7 | 2.7.11.1 | 0.452 | |
| 1kv1 | BMU | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 1mdl | SMN | Mandelate racemase | / | 0.452 | |
| 1rfq | LAR | Actin, alpha skeletal muscle | / | 0.452 | |
| 1z6p | 194 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.452 | |
| 2rgc | GNP | GTPase HRas | / | 0.452 | |
| 3cfo | GMP | DNA-directed DNA polymerase | / | 0.452 | |
| 3fzs | B96 | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.452 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2f4j | VX6 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.451 | |
| 2vwc | BC2 | ATP-dependent molecular chaperone HSP82 | / | 0.451 | |
| 2xk7 | 30E | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.451 | |
| 3sa2 | 7DR | Dihydrofolate reductase | / | 0.451 | |
| 4a4o | 664 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.451 | |
| 4o71 | CPB | Bromodomain-containing protein 4 | / | 0.451 | |
| 4a4x | JUP | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.450 | |
| 1e3v | DXC | Steroid Delta-isomerase | 5.3.3.1 | 0.449 | |
| 1ove | 358 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 2vi5 | Y19 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 3c3c | CDP | Phosphoglycerate kinase 1 | 2.7.2.3 | 0.449 | |
| 4afe | GGY | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.449 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.448 | |
| 1n5s | ADL | ActVA 6 protein | / | 0.448 | |
| 2jlb | UDM | Uncharacterized protein | / | 0.448 | |
| 2rge | GNP | GTPase HRas | / | 0.448 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.448 | |
| 4dlx | GNP | GTPase HRas | / | 0.448 | |
| 2od7 | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.447 | |
| 2xk3 | XK3 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.447 | |
| 2xk4 | OL2 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.447 | |
| 3gi3 | B10 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3l9h | ADP | Kinesin-like protein KIF11 | / | 0.447 | |
| 3mcy | ZH1 | FimH | / | 0.447 | |
| 3x04 | GNP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.447 | |
| 4h03 | NAD | Iota toxin component Ia | / | 0.447 | |
| 1f28 | F89 | Thymidylate synthase | 2.1.1.45 | 0.446 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.446 | |
| 3dne | LL1 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 3ef5 | DGT | Probable pyrophosphohydrolase | / | 0.446 | |
| 3mde | CO8 | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.446 | |
| 3oxk | 5GP | Histidine triad nucleotide-binding protein | 3 | 0.446 | |
| 3vhe | 42Q | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.446 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.446 | |
| 1s3w | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3fpb | ATP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.445 | |
| 3htj | ET | EbrA repressor | / | 0.445 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.445 | |
| 3qpg | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.445 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.445 | |
| 4y6n | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.445 | |
| 1dpm | EBP | Parathion hydrolase | 3.1.8.1 | 0.444 | |
| 1lhv | NOG | Sex hormone-binding globulin | / | 0.444 | |
| 1mqb | ANP | Ephrin type-A receptor 2 | 2.7.10.1 | 0.444 | |
| 1oh0 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.444 | |
| 3a4l | ANP | L-seryl-tRNA(Sec) kinase | 2.7.1.164 | 0.444 | |
| 3arz | I5I | Chitinase A | / | 0.444 | |
| 3cwk | REA | Cellular retinoic acid-binding protein 2 | / | 0.444 | |
| 3lbi | GNP | GTPase HRas | / | 0.444 | |
| 3rv3 | ADP | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 3w8z | HTK | Putative FAD-dependent oxygenase EncM | / | 0.444 | |
| 4at5 | MUJ | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.444 | |
| 4kao | KAO | Focal adhesion kinase 1 | 2.7.10.2 | 0.444 | |
| 4kyh | ZST | Lactoylglutathione lyase | 4.4.1.5 | 0.444 | |
| 4p66 | MTX | Dihydrofolate reductase | / | 0.444 | |
| 4ple | CPS | Nuclear receptor subfamily 5 group A member 2 | / | 0.444 | |
| 4pu2 | PLU | Aminopeptidase N | / | 0.444 | |
| 4qo9 | 627 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.444 | |
| 4x81 | MVI | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.444 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.444 | |
| 1dr4 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1p16 | GTP | mRNA-capping enzyme subunit alpha | 2.7.7.50 | 0.443 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.443 | |
| 1yho | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1z6q | 195 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.443 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.443 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 2yis | YIS | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3js2 | VM1 | Fibroblast growth factor receptor 1 | / | 0.443 | |
| 3p78 | P78 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3vri | 1KX | HLA class I histocompatibility antigen, B-57 alpha chain | / | 0.443 | |
| 3x2f | NAI | Adenosylhomocysteinase | / | 0.443 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 4lvt | 1XJ | Apoptosis regulator Bcl-2 | / | 0.443 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.443 | |
| 1x01 | ATP | 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase | / | 0.442 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.442 | |
| 2o2m | LI0 | Bcl-2-like protein 1 | / | 0.442 | |
| 2p0a | ANP | Synapsin-3 | / | 0.442 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 3d5w | ADP | Serine/threonine-protein kinase PLK | / | 0.442 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3juq | AKD | Phenazine biosynthesis protein A/B | / | 0.442 | |
| 3nf8 | CDQ | Gag-Pol polyprotein | / | 0.442 | |
| 3p7c | P7C | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 4h1j | 0YH | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.442 | |
| 4mm4 | 8PR | Na(+):neurotransmitter symporter (Snf family) | / | 0.442 | |
| 4z17 | PEP | Enolase | / | 0.442 | |
| 5ans | RX8 | 7,8-dihydro-8-oxoguanine triphosphatase | 3.6.1.55 | 0.442 | |
| 1xpc | AIT | Estrogen receptor | / | 0.441 | |
| 2io6 | 330 | Wee1-like protein kinase | 2.7.10.2 | 0.441 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.441 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.441 | |
| 3sgl | SAM | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.441 | |
| 4ho6 | UPG | Glucose-1-phosphate thymidylyltransferase | / | 0.441 | |
| 3k90 | A8S | Abscisic acid receptor PYR1 | / | 0.440 | |
| 3qrt | X14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 3rs4 | GNP | GTPase HRas | / | 0.440 | |
| 4af3 | VX6 | Aurora kinase B | 2.7.11.1 | 0.440 | |
| 4bdo | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.440 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4p68 | MTX | Dihydrofolate reductase | / | 0.440 | |
| 4uog | YYY | Nucleoside diphosphate kinase | / | 0.440 | |
| 4y6u | UPG | Glucosyl-3-phosphoglycerate synthase | 2.4.1.266 | 0.440 | |
| 4yp0 | 5IQ | Histidyl-tRNA synthetase, putative | / | 0.440 |