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 |
|---|---|---|---|
| 1ih7 | GMP | DNA-directed DNA polymerase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1ih7 | GMP | DNA-directed DNA polymerase | / | 1.000 | |
| 1clq | GDP | DNA-directed DNA polymerase | / | 0.648 | |
| 4i9q | XG4 | DNA-directed DNA polymerase | / | 0.599 | |
| 1waj | 5GP | DNA-directed DNA polymerase | / | 0.595 | |
| 3cfo | GMP | DNA-directed DNA polymerase | / | 0.549 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.505 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.493 | |
| 1pxg | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.492 | |
| 3koz | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.490 | |
| 3x02 | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.489 | |
| 2clh | F19 | Tryptophan synthase alpha chain | / | 0.488 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.485 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.482 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.477 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.477 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.476 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.476 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.476 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.475 | |
| 2bak | AQZ | Mitogen-activated protein kinase 14 | / | 0.475 | |
| 4a9y | AQZ | Mitogen-activated protein kinase 14 | / | 0.475 | |
| 3kp0 | Z98 | D-ornithine 4,5-aminomutase subunit beta | / | 0.474 | |
| 3x0a | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.474 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.473 | |
| 2wky | IBC | Glutamate receptor ionotropic, kainate 1 | / | 0.473 | |
| 4gt8 | ADP | Sensor protein VraS | 2.7.13.3 | 0.472 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.470 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.469 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.467 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.466 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.466 | |
| 3b5i | SAH | Indole-3-acetate O-methyltransferase 1 | / | 0.465 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.464 | |
| 2qmz | LDP | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.463 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.462 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.462 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.462 | |
| 4lez | 1SY | Cyclic GMP-AMP synthase | / | 0.462 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.461 | |
| 2q0k | NAP | Thioredoxin reductase | 1.8.1.9 | 0.461 | |
| 2v8p | CDP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.461 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.460 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.460 | |
| 4diq | PD2 | Ribosomal oxygenase 1 | / | 0.459 | |
| 4khn | XG4 | DNA-directed DNA polymerase | / | 0.459 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.459 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.458 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 4i9z | 5BA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.458 | |
| 4ysw | NAI | Xanthine dehydrogenase/oxidase | / | 0.458 | |
| 4zas | TYD | CalS13 | / | 0.458 | |
| 3h03 | UBP | Glutamate receptor 2 | / | 0.457 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.456 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.456 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.455 | |
| 3o9p | MHI | Periplasmic murein peptide-binding protein | / | 0.455 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.455 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.455 | |
| 1ra2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.454 | |
| 3cr0 | 809 | Wee1-like protein kinase | 2.7.10.2 | 0.454 | |
| 3sc1 | 3S1 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.454 | |
| 4hni | 16W | Casein kinase I isoform epsilon | 2.7.11.1 | 0.454 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1kmy | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.453 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.453 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.453 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.453 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.453 | |
| 3v0m | 5GW | Histo-blood group ABO system transferase | / | 0.453 | |
| 1rp4 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.452 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 3mp3 | HGG | Hydroxymethylglutaryl-CoA lyase, mitochondrial | 4.1.3.4 | 0.452 | |
| 3sso | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.452 | |
| 4ivq | I43 | Thymidine kinase | / | 0.452 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.451 | |
| 2owb | 626 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.451 | |
| 3cs9 | NIL | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.451 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.451 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.451 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.451 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.450 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.449 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.449 | |
| 3q2j | CKI | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.449 | |
| 3rl4 | 5GP | Metallophosphoesterase MPPED2 | 3.1 | 0.449 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.449 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.449 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.449 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 2xkf | BX1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.448 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 2z1w | BDI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.448 | |
| 3d3p | 20A | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 4a5l | NDP | Thioredoxin reductase | / | 0.448 | |
| 4ajm | 3A6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4gh3 | 0EV | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.448 | |
| 4kc1 | WS1 | Histo-blood group ABO system transferase | / | 0.448 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 4yqf | GDP | Septin-9 | / | 0.448 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.447 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.447 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.447 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4mt9 | 2D6 | Tankyrase-1 | 2.4.2.30 | 0.447 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.447 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.446 | |
| 2q0l | NAP | Thioredoxin reductase | 1.8.1.9 | 0.446 | |
| 2v1a | FMN | NPH1-1 | / | 0.446 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.446 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.446 | |
| 2yit | YIT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.446 | |
| 3lpf | Z77 | Beta-glucuronidase | 3.2.1.31 | 0.446 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4l23 | X6K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.446 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.446 | |
| 1e2j | THM | Thymidine kinase | / | 0.445 | |
| 1p4a | PCP | Pur operon repressor | / | 0.445 | |
| 2jgb | MGT | Eukaryotic translation initiation factor 4E type 2 | / | 0.445 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.445 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.445 | |
| 4rtj | SFG | DNA adenine methylase | 2.1.1.72 | 0.445 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.445 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.445 | |
| 1e2n | RCA | Thymidine kinase | / | 0.444 | |
| 1pyd | TDP | Pyruvate decarboxylase isozyme 1 | / | 0.444 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.444 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3cgc | COA | Coenzyme A disulfide reductase | / | 0.444 | |
| 3n0y | APC | Adenylate cyclase 2 | / | 0.444 | |
| 4fev | PP1 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.444 | |
| 4hf4 | 15H | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 5kbw | RBF | Riboflavin transporter RibU | / | 0.444 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 3lfz | ADP | Uncharacterized protein MJ1225 | / | 0.443 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 4jbx | SK7 | Thymidine kinase | / | 0.443 | |
| 4uof | DAT | Nucleoside diphosphate kinase | / | 0.443 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.443 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.443 | |
| 8cat | NDP | Catalase | 1.11.1.6 | 0.443 | |
| 1efz | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.442 | |
| 2amb | 17H | Androgen receptor | / | 0.442 | |
| 2h00 | SAH | U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase | / | 0.442 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.442 | |
| 3tp0 | FO5 | HTH-type transcriptional regulator EthR | / | 0.442 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.442 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1zyd | ATP | eIF-2-alpha kinase GCN2 | / | 0.441 | |
| 2xvu | 9DN | Serum albumin | / | 0.441 | |
| 2z2w | 770 | Wee1-like protein kinase | 2.7.10.2 | 0.441 | |
| 3x0c | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.441 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.441 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4k97 | ATP | Cyclic GMP-AMP synthase | / | 0.441 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 5hq8 | SAH | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.441 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.440 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3ftx | RE2 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.440 | |
| 3fun | 798 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.440 | |
| 3mes | PT3 | Putative choline kinase | / | 0.440 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4bdr | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.440 |