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 |
|---|---|---|---|
| 2q72 | IXX | Na(+):neurotransmitter symporter (Snf family) |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2q72 | IXX | Na(+):neurotransmitter symporter (Snf family) | / | 1.000 | |
| 2qju | DSM | Na(+):neurotransmitter symporter (Snf family) | / | 0.659 | |
| 2qei | CXX | Na(+):neurotransmitter symporter (Snf family) | / | 0.605 | |
| 2q6h | CXX | Na(+):neurotransmitter symporter (Snf family) | / | 0.602 | |
| 3gww | SFX | Na(+):neurotransmitter symporter (Snf family) | / | 0.594 | |
| 2q3e | UPG | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.491 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.485 | |
| 3gwu | SRE | Na(+):neurotransmitter symporter (Snf family) | / | 0.482 | |
| 3fpb | ATP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.481 | |
| 3k90 | A8S | Abscisic acid receptor PYR1 | / | 0.481 | |
| 1y56 | FMN | Uncharacterized protein | / | 0.480 | |
| 1y56 | FMN | 382aa long hypothetical sarcosine oxidase | / | 0.480 | |
| 4fkl | CK2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.478 | |
| 4cqn | ILA | Leucine--tRNA ligase | / | 0.477 | |
| 4z17 | PEP | Enolase | / | 0.476 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.475 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.473 | |
| 3nh8 | DC2 | N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming) | 3.5.1.114 | 0.473 | |
| 1ywr | LI9 | Mitogen-activated protein kinase 14 | / | 0.472 | |
| 3s1c | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.469 | |
| 2ayr | L4G | Estrogen receptor | / | 0.468 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.468 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.468 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.467 | |
| 3zxs | FAD | Deoxyribodipyrimidine photolyase-related protein | / | 0.467 | |
| 3tyd | XHP | Dihydropteroate synthase | / | 0.466 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.463 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.462 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.462 | |
| 4an9 | 2P7 | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.462 | |
| 4dyp | 0MS | Nucleoprotein | / | 0.462 | |
| 1h48 | CDI | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.461 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.461 | |
| 4bqy | FNT | Egl nine homolog 1 | / | 0.461 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.461 | |
| 3rfm | CFF | Adenosine receptor A2a | / | 0.460 | |
| 2b0q | ADP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.459 | |
| 3fpb | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.459 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3pzc | COA | Amino acid--[acyl-carrier-protein] ligase 1 | 6.2.1.n2 | 0.459 | |
| 3n0y | APC | Adenylate cyclase 2 | / | 0.457 | |
| 3p79 | P79 | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.457 | |
| 3ex8 | AIF | Riboflavin biosynthesis protein RibD | 1.1.1.193 | 0.456 | |
| 2wb5 | VGB | O-GlcNAcase NagJ | / | 0.455 | |
| 3c3e | FO1 | 2-phospho-L-lactate transferase | / | 0.455 | |
| 3hf6 | LX0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.455 | |
| 3k14 | 535 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.455 | |
| 4u0o | MTA | Lipoyl synthase 2 | / | 0.455 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 2vku | DBE | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.454 | |
| 3e8n | VRA | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.454 | |
| 4da4 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.454 | |
| 4deg | 0JJ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.454 | |
| 2jav | 5Z5 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.453 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.453 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.452 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.452 | |
| 3gi3 | B10 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 4bgb | ADP | Predicted molecular chaperone distantly related to HSP70-fold metalloproteases | / | 0.452 | |
| 4h03 | LAR | Actin, alpha skeletal muscle | / | 0.452 | |
| 1bl6 | SB6 | Mitogen-activated protein kinase 14 | / | 0.451 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2hek | GDP | Uncharacterized protein | / | 0.451 | |
| 2oji | 33A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.451 | |
| 4c1f | X8Z | Metallo-beta-lactamase type 2 | / | 0.451 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.451 | |
| 4i4e | 1BQ | Focal adhesion kinase 1 | 2.7.10.2 | 0.451 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.451 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.451 | |
| 2v52 | LAB | Actin, alpha skeletal muscle | / | 0.450 | |
| 4lg5 | A1O | Abscisic acid receptor PYL2 | / | 0.450 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 1kv2 | B96 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.449 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 3k3j | F4C | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 1qnf | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.448 | |
| 1wbs | LI2 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 2x7g | PVB | SRSF protein kinase 2 | 2.7.11.1 | 0.448 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.448 | |
| 2yyu | C5P | Orotidine 5'-phosphate decarboxylase | / | 0.448 | |
| 3cwk | REA | Cellular retinoic acid-binding protein 2 | / | 0.448 | |
| 4fmq | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.448 | |
| 4mv3 | ACP | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1pxo | CK7 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 1rx4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.447 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.447 | |
| 2mjp | ANP | dITP/XTP pyrophosphatase | 3.6.1.19 | 0.447 | |
| 2qqf | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.447 | |
| 2yoh | WMJ | Thymidylate kinase | / | 0.447 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.447 | |
| 4jrv | KJV | Epidermal growth factor receptor | 2.7.10.1 | 0.447 | |
| 4k9y | K9Y | Focal adhesion kinase 1 | 2.7.10.2 | 0.447 | |
| 5fs9 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.447 | |
| 1szc | CNA | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.446 | |
| 2fme | 3QC | Kinesin-like protein KIF11 | / | 0.446 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2z1w | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.446 | |
| 3i58 | 7NA | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase | / | 0.446 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.446 | |
| 3wti | CT4 | Acetylcholine-binding protein | / | 0.446 | |
| 4onq | SFG | DNA methyltransferase | / | 0.446 | |
| 5ero | 210 | Fusicoccadiene synthase | 2.5.1.29 | 0.446 | |
| 1ao0 | ADP | Amidophosphoribosyltransferase | / | 0.445 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 4kf1 | HT5 | Aryldialkylphosphatase | 3.1.8.1 | 0.445 | |
| 5bsr | COA | 4-coumarate--CoA ligase 2 | 6.2.1.12 | 0.445 | |
| 1fr8 | GDU | Beta-1,4-galactosyltransferase 1 | / | 0.444 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.444 | |
| 2c92 | TP6 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2jas | DTP | Deoxyguanosine kinase | / | 0.444 | |
| 2pwl | ACP | Fibroblast growth factor receptor 2 | / | 0.444 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3qyz | Z8B | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 3tvq | DQH | Multifunctional cyclase-dehydratase-3-O-methyl transferase TcmN | 2.1.1 | 0.444 | |
| 4eqc | XR1 | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.444 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.444 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1n5s | ADL | ActVA 6 protein | / | 0.443 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.443 | |
| 2bo7 | GDP | Mannosylglycerate synthase | / | 0.443 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3nf8 | CDQ | Gag-Pol polyprotein | / | 0.443 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.443 | |
| 4iji | 99T | Glutathione S-transferase-like protein YibF | / | 0.443 | |
| 4ixe | IXE | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1bmk | SB5 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 1jdb | ADP | Carbamoyl-phosphate synthase large chain | / | 0.442 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1z6p | 194 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.442 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 3aw9 | GDU | NAD-dependent epimerase/dehydratase | / | 0.442 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.442 | |
| 3k3k | A8S | Abscisic acid receptor PYR1 | / | 0.442 | |
| 4ful | 0VU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4l0o | PLP | Cystathionine gamma-synthase | 2.5.1.48 | 0.442 | |
| 4nt0 | 3DU | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.442 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 2cdu | FAD | NADH oxidase | / | 0.441 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.441 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3gxo | MQA | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.441 | |
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 | 0.441 | |
| 3nnu | EDB | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3nnx | EDD | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3wyg | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.441 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4a4z | ANP | Antiviral helicase SKI2 | 3.6.4.13 | 0.441 | |
| 4c9o | CAM | Cytochrome P450 | / | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 4icy | FAD | PgaE | / | 0.441 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.441 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.441 | |
| 1ltz | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.440 | |
| 1oh0 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.440 | |
| 2czf | XMP | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.440 | |
| 3h2n | B62 | Dihydropteroate synthase | / | 0.440 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.440 | |
| 3wo0 | ADP | Alanine--anticapsin ligase | / | 0.440 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.440 | |
| 4h0t | LAR | Actin, alpha skeletal muscle | / | 0.440 | |
| 4txi | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.440 | |
| 4ysw | NAI | Xanthine dehydrogenase/oxidase | / | 0.440 |