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 |
|---|---|---|---|
| 4bmo | FMN | Protein NrdI |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4bmo | FMN | Protein NrdI | / | 1.000 | |
| 4bmp | FMN | Protein NrdI | / | 0.654 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.501 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.498 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.492 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.488 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.485 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.482 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.478 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.477 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.476 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.473 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.472 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.469 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.468 | |
| 4iae | 1DX | Alr2278 protein | / | 0.468 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.468 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.467 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.467 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 4ike | ADP | Adenylate kinase | / | 0.467 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.467 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.466 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.466 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.464 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.464 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.464 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.464 | |
| 4l4x | NDP | AmphI | / | 0.463 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.463 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.463 | |
| 3jzi | JZL | Biotin carboxylase | 6.3.4.14 | 0.462 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.461 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.461 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.461 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.461 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.460 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.460 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.460 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.460 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.459 | |
| 3bnk | FMN | Flavoredoxin | / | 0.459 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.459 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.458 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 3oht | 1N1 | Mitogen-activated protein kinase | / | 0.458 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.457 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.457 | |
| 3ncr | ADP | Nitrogen regulatory protein P-II (GlnB-2) | / | 0.457 | |
| 4jld | ADP | Adenylate kinase | / | 0.457 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.457 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.456 | |
| 2vzz | SCA | Putative succinyl-CoA transferase Rv0802c | 2.8.3 | 0.456 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.455 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.454 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.454 | |
| 4tyq | AP5 | Adenylate kinase | / | 0.454 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.453 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.453 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.453 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.453 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.453 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.452 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.452 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.452 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4y9u | NAP | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 1f4g | TP4 | Thymidylate synthase | / | 0.451 | |
| 1fml | RTL | Retinol dehydratase | / | 0.451 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.451 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.451 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 3n39 | FMN | Protein NrdI | / | 0.450 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.450 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.450 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.450 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.449 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4iah | 1DX | Alr2278 protein | / | 0.449 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.449 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.449 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.449 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 2ab8 | ACP | Adenosine kinase | 2.7.1.20 | 0.448 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 3b2s | B2S | Trichothecene 3-O-acetyltransferase | / | 0.448 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.448 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4jlo | ADP | Adenylate kinase | / | 0.448 | |
| 1eio | GCH | Gastrotropin | / | 0.447 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.447 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.447 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.447 | |
| 2qn3 | F55 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.447 | |
| 2y3s | TIR | TamL | / | 0.447 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.447 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3qof | GDP | Atlastin-1 | 3.6.5 | 0.447 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.447 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.446 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.446 | |
| 2ejz | SAH | Diphthine synthase | / | 0.446 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.446 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.446 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.445 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.445 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.445 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.445 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2wxv | WXV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 3exn | ACO | Probable acetyltransferase | / | 0.445 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.445 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.445 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.444 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.444 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.444 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.444 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.444 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.444 | |
| 5a3b | APR | SIR2 family protein | / | 0.444 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2ij7 | TPF | Mycocyclosin synthase | 1.14.21.9 | 0.443 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4cf7 | ADP | Adenylate kinase | / | 0.443 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.442 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.442 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.442 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.442 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.442 | |
| 4a2j | AS0 | Progesterone receptor | / | 0.442 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.442 | |
| 5a3c | NAD | SIR2 family protein | / | 0.442 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.442 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.441 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.441 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.441 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.441 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.441 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.441 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.441 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.441 | |
| 4c58 | 824 | Cyclin-G-associated kinase | 2.7.11.1 | 0.441 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.441 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.441 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1iqr | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.440 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.440 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.440 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.440 | |
| 3ih0 | ANP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.440 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.440 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.440 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.440 |