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 |
|---|---|---|---|
| 2q72 | IXX | Na(+):neurotransmitter symporter (Snf family) |
| PDB ID | HET | Uniprot Name | EC Number | Cavity 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) | / | 0.600 | |
| 3gww | SFX | Na(+):neurotransmitter symporter (Snf family) | / | 0.594 | |
| 2q3e | UPG | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.490 | |
| 3gwu | SRE | Na(+):neurotransmitter symporter (Snf family) | / | 0.481 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.480 | |
| 3k90 | A8S | Abscisic acid receptor PYR1 | / | 0.476 | |
| 2ayr | L4G | Estrogen receptor | / | 0.472 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.472 | |
| 1ywr | LI9 | Mitogen-activated protein kinase 14 | / | 0.471 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.464 | |
| 3p79 | P79 | Mitogen-activated protein kinase 14 | / | 0.464 | |
| 3k3j | F4C | Mitogen-activated protein kinase 14 | / | 0.462 | |
| 3kjs | DQ1 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.462 | |
| 1y56 | FMN | Uncharacterized protein | / | 0.461 | |
| 1y56 | FMN | 382aa long hypothetical sarcosine oxidase | / | 0.461 | |
| 3fpb | ATP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.461 | |
| 3p5k | P5K | Mitogen-activated protein kinase 14 | / | 0.461 | |
| 4bqy | FNT | Egl nine homolog 1 | / | 0.461 | |
| 3jvh | HHV | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.459 | |
| 4fkl | CK2 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.459 | |
| 4z17 | PEP | Enolase | / | 0.459 | |
| 1xid | ASC | Xylose isomerase | 5.3.1.5 | 0.458 | |
| 3tyd | XHP | Dihydropteroate synthase | / | 0.457 | |
| 2b0q | ADP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.456 | |
| 3n0y | APC | Adenylate cyclase 2 | / | 0.454 | |
| 4deg | 0JJ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.454 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.453 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.452 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.452 | |
| 1y7u | COA | Acyl-CoA hydrolase | / | 0.451 | |
| 2oji | 33A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.451 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.451 | |
| 1tez | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.450 | |
| 3nh8 | DC2 | N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming) | 3.5.1.114 | 0.450 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.450 | |
| 4h03 | LAR | Actin, alpha skeletal muscle | / | 0.450 | |
| 4i4e | 1BQ | Focal adhesion kinase 1 | 2.7.10.2 | 0.450 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.449 | |
| 2jav | 5Z5 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.449 | |
| 3gi3 | B10 | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 1qnf | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.448 | |
| 1s4e | ADP | Galactokinase | / | 0.448 | |
| 2v52 | LAB | Actin, alpha skeletal muscle | / | 0.448 | |
| 3pzc | COA | Amino acid--[acyl-carrier-protein] ligase 1 | 6.2.1.n2 | 0.448 | |
| 4fmq | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.448 | |
| 2x7g | PVB | SRSF protein kinase 2 | 2.7.11.1 | 0.447 | |
| 3eej | 53R | Uncharacterized protein | / | 0.447 | |
| 4jrv | KJV | Epidermal growth factor receptor | 2.7.10.1 | 0.447 | |
| 1bl6 | SB6 | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 1szc | CNA | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.446 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3tdk | UPG | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.446 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.446 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 2fme | 3QC | Kinesin-like protein KIF11 | / | 0.445 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.445 | |
| 4lg5 | A1O | Abscisic acid receptor PYL2 | / | 0.445 | |
| 1oz1 | FPH | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 1y8y | CT7 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 2pwl | ACP | Fibroblast growth factor receptor 2 | / | 0.444 | |
| 2y4k | GDP | Uncharacterized protein | / | 0.444 | |
| 2yoh | WMJ | Thymidylate kinase | / | 0.444 | |
| 3qyz | Z8B | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 4eqc | XR1 | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.444 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1e7a | PFL | Serum albumin | / | 0.443 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.443 | |
| 1n5s | ADL | ActVA 6 protein | / | 0.443 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.443 | |
| 2w3a | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3irn | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3k14 | 535 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.443 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.443 | |
| 4k9y | K9Y | Focal adhesion kinase 1 | 2.7.10.2 | 0.443 | |
| 4onq | SFG | DNA methyltransferase | / | 0.443 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.443 | |
| 1jdb | ADP | Carbamoyl-phosphate synthase large chain | / | 0.442 | |
| 1n5t | OAL | ActVA 6 protein | / | 0.442 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.442 | |
| 3eem | 53V | Uncharacterized protein | / | 0.442 | |
| 3k3k | A8S | Abscisic acid receptor PYR1 | / | 0.442 | |
| 1dg5 | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.441 | |
| 2z1w | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.441 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.441 | |
| 3elm | 24F | Collagenase 3 | 3.4.24 | 0.441 | |
| 3h24 | B55 | Dihydropteroate synthase | / | 0.441 | |
| 3nf8 | CDQ | Gag-Pol polyprotein | / | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 4nt0 | 3DU | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.441 | |
| 4ysw | NAI | Xanthine dehydrogenase/oxidase | / | 0.441 | |
| 1h48 | CDI | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.440 | |
| 1ltz | HBI | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.440 | |
| 1mdl | RMN | Mandelate racemase | / | 0.440 | |
| 1oh0 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.440 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1z6p | 194 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.440 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.440 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.440 | |
| 4h0t | LAR | Actin, alpha skeletal muscle | / | 0.440 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.440 |