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 |
|---|---|---|---|
| 4i3w | NAD | Aldehyde dehydrogenase (NAD+) |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4i3w | NAD | Aldehyde dehydrogenase (NAD+) | / | 1.000 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.484 | |
| 4i3v | NAD | Aldehyde dehydrogenase (NAD+) | / | 0.477 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.476 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.474 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.470 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.469 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.468 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.468 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.465 | |
| 4kb8 | 1QN | Casein kinase I isoform delta | 2.7.11.1 | 0.465 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.465 | |
| 1jvs | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.464 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.464 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.464 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.464 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.462 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.462 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.460 | |
| 2izs | BRQ | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.460 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.460 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.459 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.459 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.459 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.459 | |
| 2pvn | P63 | Casein kinase II subunit alpha | 2.7.11.1 | 0.458 | |
| 3et7 | 349 | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.458 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.458 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.457 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.456 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.456 | |
| 4ezj | 0SC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.456 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.454 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.454 | |
| 3w1f | 1O5 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.454 | |
| 4b7d | QLE | Cytochrome P450 monooxygenase PikC | / | 0.454 | |
| 4cax | MYA | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.454 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.454 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.453 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.453 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.453 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.453 | |
| 4k11 | 0J9 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.453 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1yhs | STU | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.452 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.452 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 4mcv | 29K | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.452 | |
| 2c6h | PXI | Cytochrome P450 monooxygenase PikC | / | 0.451 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.451 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.450 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.450 | |
| 3th8 | TH9 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.450 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.450 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.450 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.450 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.450 | |
| 1dnp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.449 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.449 | |
| 2hxl | 422 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.449 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.449 | |
| 3tmz | 06X | Cytochrome P450 2B4 | 1.14.14.1 | 0.449 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.449 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.449 | |
| 2brm | DFZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.448 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 3tea | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.448 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.448 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.448 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.448 | |
| 1xkk | FMM | Epidermal growth factor receptor | 2.7.10.1 | 0.447 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.447 | |
| 2hog | 710 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.447 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.447 | |
| 3ofm | 4B0 | Casein kinase II subunit alpha' | 2.7.11.1 | 0.447 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.447 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.447 | |
| 4hgt | 15G | Casein kinase I isoform delta | 2.7.11.1 | 0.447 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.447 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.446 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.446 | |
| 2hfp | NSI | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2j3i | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.446 | |
| 3l08 | ZIG | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 3lu8 | IQX | Serum albumin | / | 0.446 | |
| 3poz | 03P | Epidermal growth factor receptor | 2.7.10.1 | 0.446 | |
| 4f1s | F1S | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.446 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.446 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.445 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.445 | |
| 2xdr | NDP | NAD/NADP-dependent betaine aldehyde dehydrogenase | / | 0.445 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.445 | |
| 3r34 | COA | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.445 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.445 | |
| 3zux | TCH | Transporter | / | 0.445 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.445 | |
| 4mxx | DB8 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.445 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.444 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.444 | |
| 2qfx | NDP | Isocitrate dehydrogenase [NADP], mitochondrial | 1.1.1.42 | 0.444 | |
| 2ydi | YDI | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 3bhe | BZN | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.444 | |
| 4gk4 | L90 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.443 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.443 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.443 | |
| 3hv5 | R24 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.443 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.443 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.443 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1iid | NHM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.442 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.442 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.442 | |
| 3at4 | CCK | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.442 | |
| 3w0s | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.442 | |
| 4id7 | 1G0 | Activated CDC42 kinase 1 | / | 0.442 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.441 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1zhw | HC2 | Oxysterol-binding protein homolog 4 | / | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 2etm | 7PY | Focal adhesion kinase 1 | 2.7.10.2 | 0.441 | |
| 2j0m | 4ST | Focal adhesion kinase 1 | 2.7.10.2 | 0.441 | |
| 3iqe | F42 | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.441 | |
| 3l8p | 0CE | Angiopoietin-1 receptor | 2.7.10.1 | 0.441 | |
| 3otx | AP5 | Adenosine kinase, putative | / | 0.441 | |
| 4l9k | EHF | Serum albumin | / | 0.441 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.441 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 1nq7 | ARL | Nuclear receptor ROR-beta | / | 0.440 | |
| 1xjd | STU | Protein kinase C theta type | 2.7.11.13 | 0.440 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.440 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.440 | |
| 3ama | SKE | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3bej | MUF | Bile acid receptor | / | 0.440 | |
| 3igo | ANP | Calmodulin-domain protein kinase 1, putative | / | 0.440 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3sgx | 0FW | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.440 | |
| 4a0m | NAD | Betaine aldehyde dehydrogenase, chloroplastic | 1.2.1.8 | 0.440 | |
| 4cta | ATP | CinA-like protein | / | 0.440 | |
| 4kwi | 1TJ | Reductase homolog | / | 0.440 |