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 |
|---|---|---|---|
| 3ryr | CMP | cAMP-activated global transcriptional regulator CRP |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3ryr | CMP | cAMP-activated global transcriptional regulator CRP | / | 1.000 | |
| 2gzw | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.619 | |
| 1i6x | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.600 | |
| 4i0b | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.559 | |
| 1hw5 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.556 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.555 | |
| 1cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.542 | |
| 1g6n | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.542 | |
| 2oz6 | CMP | Cyclic AMP receptor-like protein | / | 0.531 | |
| 3mzh | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.495 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.492 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.488 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.479 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.471 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.468 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.468 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.467 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.467 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.465 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.465 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.464 | |
| 4jkt | 04A | Glutaminase kidney isoform, mitochondrial | 3.5.1.2 | 0.463 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.462 | |
| 2qu6 | 857 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.459 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.458 | |
| 2cvz | NDP | 3-hydroxyisobutyrate dehydrogenase | / | 0.458 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.458 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.457 | |
| 1k6v | XN2 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.455 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.455 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.454 | |
| 2yit | YIT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.454 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3hmm | 855 | TGF-beta receptor type-1 | 2.7.11.30 | 0.454 | |
| 4hxy | NDP | Plm1 | / | 0.454 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.453 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.453 | |
| 4f1y | CNI | Glutamate receptor 3 | / | 0.453 | |
| 1sny | NAP | LD36273p | / | 0.452 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.452 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.452 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.451 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.451 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.451 | |
| 4ng5 | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.450 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.450 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.450 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.450 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.449 | |
| 4u9a | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.449 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.448 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 1rw8 | 580 | TGF-beta receptor type-1 | 2.7.11.30 | 0.448 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.448 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.448 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.448 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.447 | |
| 2gf6 | COA | Uncharacterized protein | / | 0.447 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.447 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.447 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.447 | |
| 4loq | SB4 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 1iy8 | NAD | Levodione reductase | / | 0.446 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 2w0j | ZAT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.446 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.446 | |
| 5cno | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.446 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.445 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.445 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.445 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.445 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.445 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.445 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.445 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 5a3b | APR | SIR2 family protein | / | 0.445 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1h6d | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.444 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.444 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.444 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.444 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.444 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.444 | |
| 3nuy | JPZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.444 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.444 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.444 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.444 | |
| 5kjc | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 2b4y | APR | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.443 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.443 | |
| 2nmx | M25 | Carbonic anhydrase 1 | 4.2.1.1 | 0.443 | |
| 3qd3 | 3Q5 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.443 | |
| 4abz | T1C | Tetracycline repressor protein class D | / | 0.443 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.443 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.443 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.442 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.442 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.442 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.442 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.441 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.441 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.441 | |
| 3uqd | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.441 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.441 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.441 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.440 | |
| 2hs1 | 017 | Protease | / | 0.440 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3v3m | 0EN | Replicase polyprotein 1a | 3.4.19.12 | 0.440 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.440 |