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 |
|---|---|---|---|
| 3neg | PYV | Abscisic acid receptor PYL1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 1.000 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.561 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.559 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.556 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.548 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.541 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.534 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.533 | |
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.527 | |
| 3nef | PYV | Abscisic acid receptor PYL1 | / | 0.525 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.518 | |
| 3k3k | A8S | Abscisic acid receptor PYR1 | / | 0.516 | |
| 3nmn | PYV | Abscisic acid receptor PYL1 | / | 0.515 | |
| 3r6p | A8S | Abscisic acid receptor PYL10 | / | 0.504 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.493 | |
| 4oic | A8S | Bet v I allergen-like | / | 0.492 | |
| 1og5 | SWF | Cytochrome P450 2C9 | / | 0.489 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.489 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.489 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.486 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.485 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.480 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.480 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.479 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.479 | |
| 3kb3 | A8S | Abscisic acid receptor PYL2 | / | 0.475 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.475 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.473 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.473 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.471 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.468 | |
| 4bfr | J82 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform | 2.7.1.153 | 0.465 | |
| 1yho | TRR | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.464 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.463 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.463 | |
| 1tvr | TB9 | Gag-Pol polyprotein | 2.7.7.49 | 0.463 | |
| 3ar5 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.462 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.462 | |
| 4dk5 | 0KO | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.462 | |
| 3eek | 53S | Uncharacterized protein | / | 0.461 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 2ze2 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.460 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.460 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.460 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.459 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.459 | |
| 1s9q | OHT | Estrogen-related receptor gamma | / | 0.458 | |
| 2chw | 039 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.458 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1m8h | 6NI | Nitric oxide synthase, inducible | 1.14.13.39 | 0.457 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.457 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 1osv | CHC | Bile acid receptor | / | 0.456 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.456 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.455 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.455 | |
| 3qlh | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.455 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.455 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3cse | N22 | Uncharacterized protein | / | 0.454 | |
| 3d0b | SNX | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 3k47 | D09 | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.454 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.453 | |
| 2wle | COA | Polysialic acid O-acetyltransferase | / | 0.453 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 3qaq | QAQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 3tdl | 11D | Serum albumin | / | 0.453 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.453 | |
| 5d1b | TSN | Histone deacetylase 8 | 3.5.1.98 | 0.453 | |
| 2qgt | EED | Estrogen receptor | / | 0.452 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.452 | |
| 3eel | 53T | Uncharacterized protein | / | 0.452 | |
| 3iro | 2CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.452 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4jvl | EST | Estrogen sulfotransferase | 2.8.2.4 | 0.452 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.451 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.451 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.451 | |
| 4l23 | X6K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.451 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.450 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.450 | |
| 3qai | XNN | Ketohexokinase | / | 0.450 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.450 | |
| 1tkz | H16 | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.449 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.449 | |
| 1dv2 | ATP | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 1kyo | SMA | Cytochrome b | / | 0.448 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.448 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 3kdj | A8S | Abscisic acid receptor PYL1 | / | 0.448 | |
| 3uvv | REA | Retinoic acid receptor RXR-alpha | / | 0.448 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.448 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.447 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.447 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.446 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.446 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.446 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.446 | |
| 4eil | FOL | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.445 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.445 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.445 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3q2m | CKI | Spectinomycin phosphotransferase | / | 0.445 | |
| 3sgy | 06W | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.445 | |
| 4a9e | 3PF | Bromodomain-containing protein 2 | / | 0.445 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.445 | |
| 4v12 | POG | MaoC like domain protein | / | 0.445 | |
| 5dq8 | FLF | Transcriptional enhancer factor TEF-4 | / | 0.445 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.445 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1xu9 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3iqz | H4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.444 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 3ue4 | DB8 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.444 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.444 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4ejg | NCT | Cytochrome P450 2A13 | 1.14.14.1 | 0.444 | |
| 4ejh | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.444 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.444 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.444 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.443 | |
| 1n4h | REA | Nuclear receptor ROR-beta | / | 0.443 | |
| 2gn9 | UPG | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.443 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.443 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 4awq | 592 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.443 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.443 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1ysx | 4EB | Serum albumin | / | 0.442 | |
| 2cjm | ATP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2qe4 | JJ3 | Estrogen receptor | / | 0.442 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.442 | |
| 3qlr | QLR | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.442 | |
| 4a5y | G7X | Kinesin-like protein KIF11 | / | 0.442 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 1hnv | TBO | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.441 | |
| 2etr | Y27 | Rho-associated protein kinase 1 | 2.7.11.1 | 0.441 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2x7g | PVB | SRSF protein kinase 2 | 2.7.11.1 | 0.441 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.441 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3iqf | E4M | F420-dependent methylenetetrahydromethanopterin dehydrogenase | 1.5.98.1 | 0.441 | |
| 3lu8 | IQX | Serum albumin | / | 0.441 | |
| 4k5y | 1Q5 | Corticotropin-releasing factor receptor 1 | / | 0.441 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.440 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.440 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 2y46 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.440 | |
| 3l08 | ZIG | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3lak | KR1 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.440 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.440 | |
| 4dvq | 1CA | Cytochrome P450 11B2, mitochondrial | 1.14.15.4 | 0.440 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4kfj | 1R0 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.440 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.440 |