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 |
|---|---|---|---|
| 2dxf | GNP | Nucleoside diphosphate kinase | 2.7.4.6 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2dxf | GNP | Nucleoside diphosphate kinase | 2.7.4.6 | 1.000 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.613 | |
| 1nue | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.570 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.570 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.566 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.548 | |
| 1bux | PPS | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.531 | |
| 2dy9 | ADP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.515 | |
| 4uoh | ADP | Nucleoside diphosphate kinase | / | 0.505 | |
| 1wkl | ATP | Nucleoside diphosphate kinase | / | 0.498 | |
| 2az3 | CDP | Nucleoside diphosphate kinase | / | 0.497 | |
| 3ngu | ADP | Nucleoside diphosphate kinase | / | 0.490 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.490 | |
| 4hr2 | ADP | Nucleoside diphosphate kinase | / | 0.489 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.484 | |
| 1uhh | CZP | Aequorin-2 | / | 0.483 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.482 | |
| 2dxe | GDP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.482 | |
| 4olf | HFG | Proline--tRNA ligase | 6.1.1.15 | 0.482 | |
| 1zs6 | ADP | Nucleoside diphosphate kinase 3 | 2.7.4.6 | 0.480 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.478 | |
| 4jva | 1OR | cAMP-dependent protein kinase type II-beta regulatory subunit | / | 0.478 | |
| 1be4 | PCG | Nucleoside diphosphate kinase A 2 | 2.7.4.6 | 0.476 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.476 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.476 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.476 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.475 | |
| 4uof | DAT | Nucleoside diphosphate kinase | / | 0.474 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.473 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.472 | |
| 4dlc | UMP | Deoxyuridine triphosphatase, putative | / | 0.469 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.468 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.467 | |
| 3bgx | TMP | Thymidylate synthase | / | 0.467 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.467 | |
| 1ndc | TYD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.466 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.465 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.465 | |
| 9mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.465 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.464 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.464 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.464 | |
| 2e91 | ZOL | Geranylgeranyl pyrophosphate synthase | / | 0.461 | |
| 4lb9 | EVP | Serum albumin | / | 0.461 | |
| 4nqg | CZH | Mitrocomin | / | 0.461 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.460 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.459 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.458 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.457 | |
| 1ej3 | CZH | Aequorin-2 | / | 0.456 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.456 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.455 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.455 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.454 | |
| 4phl | PIL | Phosphodiesterase | / | 0.454 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.454 | |
| 1h6b | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.453 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.453 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.453 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.453 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.453 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.452 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.452 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.452 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.452 | |
| 3dcw | EZL | Carbonic anhydrase 2 | 4.2.1.1 | 0.452 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.452 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.452 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.451 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.451 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 2hvd | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.451 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.451 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.451 | |
| 3gxf | IFM | Glucosylceramidase | 3.2.1.45 | 0.451 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.451 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.450 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.450 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.449 | |
| 2cje | DUN | DUTPase | / | 0.449 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3v0m | 5GW | Histo-blood group ABO system transferase | / | 0.449 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.449 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.448 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.448 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.448 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.448 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 4kc1 | WS1 | Histo-blood group ABO system transferase | / | 0.448 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.448 | |
| 5agy | GTB | Tau class glutathione S-transferase | / | 0.448 | |
| 1mv8 | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.447 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.447 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 1n95 | FTH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.446 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.446 | |
| 2wey | EV1 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 3pn1 | IVH | DNA ligase | / | 0.446 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.446 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.445 | |
| 1tl3 | H20 | Gag-Pol polyprotein | 2.7.7.49 | 0.445 | |
| 2wzg | UPG | Uncharacterized protein | / | 0.445 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.445 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.445 | |
| 1cg6 | MTA | S-methyl-5'-thioadenosine phosphorylase | / | 0.444 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.444 | |
| 2ovy | PFJ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 2vfz | UPF | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.444 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4hyv | PEP | Pyruvate kinase 1 | 2.7.1.40 | 0.444 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.444 | |
| 1csc | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.443 | |
| 1e0j | ANP | DNA primase/helicase | 2.7.7 | 0.443 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.443 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.443 | |
| 2i5n | UQ1 | Reaction center protein L chain | / | 0.443 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 3o0i | P54 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.443 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.443 | |
| 4mvh | 2F5 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1d2s | DHT | Sex hormone-binding globulin | / | 0.442 | |
| 1el4 | CTZ | Obelin | / | 0.442 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 1s36 | CEI | Obelin | / | 0.442 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.442 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4zwm | PLP | Ornithine aminotransferase, mitochondrial, putative | / | 0.442 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.441 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1xdp | ATP | Polyphosphate kinase | / | 0.441 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3fow | IMH | Purine nucleoside phosphorylase | / | 0.441 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.441 | |
| 3lfz | ADP | Uncharacterized protein MJ1225 | / | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.441 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.440 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.440 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2pvy | ACP | Fibroblast growth factor receptor 2 | / | 0.440 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.440 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.440 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.440 |