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 |
|---|---|---|---|
| 4bmp | FMN | Protein NrdI |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4bmp | FMN | Protein NrdI | / | 1.000 | |
| 4bmo | FMN | Protein NrdI | / | 0.635 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.494 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.491 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.490 | |
| 3n39 | FMN | Protein NrdI | / | 0.490 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.490 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.487 | |
| 1p7t | ACO | Malate synthase G | / | 0.485 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.478 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.476 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.475 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.471 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.471 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.470 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.468 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.463 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1xds | DRA | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.461 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.461 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.461 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.461 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.458 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.458 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.458 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.458 | |
| 3ih0 | ANP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.457 | |
| 4p6x | HCY | Glucocorticoid receptor | / | 0.457 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 2ejz | SAH | Diphthine synthase | / | 0.456 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.456 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.455 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.453 | |
| 1m9m | 6NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.453 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2vmy | FFO | Serine hydroxymethyltransferase | / | 0.453 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.451 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.451 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.451 | |
| 3qpv | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.451 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.451 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.450 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.450 | |
| 2huv | SAH | Diphthine synthase | / | 0.450 | |
| 3n3b | FMN | Protein NrdI | / | 0.450 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.449 | |
| 2e08 | SAH | Diphthine synthase | / | 0.449 | |
| 3mtf | A3F | Activin receptor type-1 | 2.7.11.30 | 0.449 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.449 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.448 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.448 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.448 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.448 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.448 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.448 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.447 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.447 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.446 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.446 | |
| 2nr4 | FMN | Conserved protein | / | 0.446 | |
| 2xvq | 9DS | Serum albumin | / | 0.446 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.446 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.446 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.446 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.446 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.445 | |
| 2qpy | DHT | Androgen receptor | / | 0.445 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.445 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.445 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.444 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 1osv | CHC | Bile acid receptor | / | 0.444 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.444 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.444 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.444 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.443 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.443 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.443 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1mzn | BM6 | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 1p93 | DEX | Glucocorticoid receptor | / | 0.442 | |
| 2y3s | TIR | TamL | / | 0.442 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 4a2j | AS0 | Progesterone receptor | / | 0.442 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.442 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.442 | |
| 4k7a | DHT | Androgen receptor | / | 0.442 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1i58 | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.441 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.441 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2jfg | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.441 | |
| 2npi | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.441 | |
| 2w3m | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.441 | |
| 3gob | HXX | DdmC | / | 0.441 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.441 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.441 | |
| 4h97 | 53S | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.441 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.440 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.440 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.440 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.440 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.440 |