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 |
|---|---|---|---|
| 5iub | CLR | Adenosine receptor A2a |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5iub | CLR | Adenosine receptor A2a | / | 1.000 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.795 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.769 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.706 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.692 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.675 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.659 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.656 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.649 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.644 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.642 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.629 | |
| 2ydv | NEC | Adenosine receptor A2a | / | 0.582 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.581 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.560 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.531 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.526 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.517 | |
| 1a4i | NDP | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.498 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.492 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.485 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.482 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.479 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.477 | |
| 3uza | T4G | Adenosine receptor A2a | / | 0.477 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.471 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.469 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 4ejn | 0R4 | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.467 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 5dp2 | NAP | CurF | / | 0.465 | |
| 4jv4 | 1OR | cAMP-dependent protein kinase type I-alpha regulatory subunit | / | 0.464 | |
| 2f4j | VX6 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.461 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.461 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.460 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.460 | |
| 1osv | CHC | Bile acid receptor | / | 0.459 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 3h4v | DVP | Pteridine reductase 1 | 1.5.1.33 | 0.459 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.459 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.459 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.459 | |
| 3be2 | RAJ | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.458 | |
| 2vwx | 7X4 | Ephrin type-B receptor 4 | 2.7.10.1 | 0.457 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.457 | |
| 4nc3 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.457 | |
| 4ea3 | 0NN | Nociceptin receptor | / | 0.457 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.456 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.455 | |
| 2zb1 | GK4 | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.455 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4equ | G6I | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.454 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.454 | |
| 5hbs | RTL | Retinol-binding protein 1 | / | 0.454 | |
| 3oez | STI | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.453 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.453 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.453 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2bfp | H4B | Pteridine reductase 1 | 1.5.1.33 | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.452 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.452 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.452 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.451 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.450 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.450 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2iea | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.449 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.449 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.449 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.449 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.449 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.449 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.448 | |
| 1e92 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.448 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.448 | |
| 3cqe | P91 | Wee1-like protein kinase | 2.7.10.2 | 0.448 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3sl8 | JN7 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.448 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4l4x | NDP | AmphI | / | 0.448 | |
| 4lb2 | DM5 | Serum albumin | / | 0.448 | |
| 4pd6 | URI | Nucleoside permease | / | 0.448 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.448 | |
| 1l2j | ETC | Estrogen receptor beta | / | 0.447 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.447 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.447 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1u0h | ONM | Adenylate cyclase type 2 | / | 0.446 | |
| 1u0h | ONM | Adenylate cyclase type 5 | / | 0.446 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3cwk | REA | Cellular retinoic acid-binding protein 2 | / | 0.446 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1fml | RTL | Retinol dehydratase | / | 0.445 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.445 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.445 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.445 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3up0 | D7S | aceDAF-12 | / | 0.445 | |
| 1e2j | THM | Thymidine kinase | / | 0.444 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.444 | |
| 2gfs | PQB | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 2qd5 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.444 | |
| 3vs6 | VSH | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.444 | |
| 3znq | SS8 | D-amino-acid oxidase | 1.4.3.3 | 0.444 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 4dgg | I76 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.444 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.444 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.443 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.443 | |
| 3h4v | NAP | Pteridine reductase 1 | 1.5.1.33 | 0.443 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.443 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 3vs4 | VSF | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.443 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1qkn | RAL | Estrogen receptor beta | / | 0.442 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.442 | |
| 1xkd | NAP | Isocitrate dehydrogenase [NADP] | / | 0.442 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.442 | |
| 2fsz | OHT | Estrogen receptor beta | / | 0.442 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.442 | |
| 3b8r | 887 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.442 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.441 | |
| 3fnh | JPJ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.441 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4fic | 0UL | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.441 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.440 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3qfc | NAP | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.440 | |
| 4gki | 0JN | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.440 | |
| 4okx | 198 | Androgen receptor | / | 0.440 |