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 |
|---|---|---|---|
| 2oz6 | CMP | Cyclic AMP receptor-like protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2oz6 | CMP | Cyclic AMP receptor-like protein | / | 1.000 | |
| 3n4m | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.582 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.557 | |
| 1hw5 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.504 | |
| 3ryr | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.484 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.482 | |
| 3t3c | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.477 | |
| 3tuc | FPW | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.477 | |
| 4i09 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.477 | |
| 4i01 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.474 | |
| 1m17 | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.473 | |
| 3ryp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.473 | |
| 4i0a | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.473 | |
| 1cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.472 | |
| 3od0 | PCG | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.469 | |
| 3u0z | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 | / | 0.469 | |
| 3cl1 | PCG | Cyclic nucleotide-gated potassium channel mll3241 | / | 0.468 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.468 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.467 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.467 | |
| 3kcc | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.466 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.465 | |
| 3ocp | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.462 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.462 | |
| 1xl2 | 189 | Gag-Pol polyprotein | 3.4.23.16 | 0.461 | |
| 3el9 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 4hzf | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.460 | |
| 1q3e | PCG | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | / | 0.459 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.459 | |
| 2y4g | TIR | TamL | / | 0.458 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.458 | |
| 5dn3 | ATP | Aurora kinase A | 2.7.11.1 | 0.458 | |
| 1ruo | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.457 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.457 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.457 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.456 | |
| 2gzw | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.456 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.455 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.455 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.455 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.455 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.455 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.455 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.455 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1zar | ADP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.454 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.454 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.454 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.454 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.453 | |
| 1jvs | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.451 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3ngl | NAP | Bifunctional protein FolD | / | 0.451 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.451 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.451 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.451 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 1q43 | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 | / | 0.450 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.450 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.450 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.450 | |
| 2zb0 | GK3 | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.450 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.450 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.450 | |
| 2xye | CXG | Gag-Pol polyprotein | / | 0.449 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.449 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.449 | |
| 4bqh | 9VU | UDP-N-acetylglucosamine pyrophosphorylase, putative | / | 0.449 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 1uu9 | BI3 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.448 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.448 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.448 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1heu | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1u59 | STU | Tyrosine-protein kinase ZAP-70 | 2.7.10.2 | 0.447 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.447 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.447 | |
| 4d7t | CMP | Uncharacterized protein | / | 0.447 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.446 | |
| 1t1r | IMB | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.446 | |
| 1uu7 | BI2 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 3ckt | YDP | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.446 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4z07 | PCG | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.446 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.445 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.445 | |
| 3qop | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.445 | |
| 1osv | CHC | Bile acid receptor | / | 0.444 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2k0g | CMP | Cyclic nucleotide-gated potassium channel mll3241 | / | 0.444 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.444 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.444 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.444 | |
| 3r37 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.444 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.444 | |
| 4i0b | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.444 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1vp6 | CMP | Cyclic nucleotide-gated potassium channel mll3241 | / | 0.443 | |
| 2bdf | 24A | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.443 | |
| 2f3k | RO1 | Protease | / | 0.443 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.443 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.442 | |
| 1yol | S03 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.442 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.442 | |
| 2pvy | ACP | Fibroblast growth factor receptor 2 | / | 0.442 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.442 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.441 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2g2z | COZ | Malonyl CoA-acyl carrier protein transacylase | 2.3.1.39 | 0.441 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.441 | |
| 3b2e | ADP | ATPase GET3 | / | 0.441 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3eej | 53R | Uncharacterized protein | / | 0.441 | |
| 3nxe | 2NC | Protease | / | 0.441 | |
| 3poz | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 3t11 | 3T1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.441 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.441 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.441 | |
| 4lht | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.441 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.441 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 1kzk | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 2xyf | G40 | Gag-Pol polyprotein | / | 0.440 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.440 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.440 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.440 |