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 |
|---|---|---|---|
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 1.000 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.657 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.640 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.627 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.615 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.614 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.612 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.604 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.600 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.599 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.562 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.551 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.510 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.506 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.488 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.488 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.488 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.487 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.485 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.480 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.473 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.472 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.472 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.471 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.470 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.470 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.469 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.469 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.468 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.467 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.466 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.466 | |
| 1zp4 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.465 | |
| 1aa6 | MGD | Formate dehydrogenase H | 1.1.99.33 | 0.464 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.464 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.464 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.464 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.463 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.463 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.462 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.462 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.462 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.462 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.462 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.461 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.460 | |
| 1k4q | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.460 | |
| 2h2a | DND | Probable nicotinate-nucleotide adenylyltransferase | / | 0.460 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.460 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 1p0f | NAP | NADP-dependent alcohol dehydrogenase | 1.1.1.2 | 0.459 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.459 | |
| 3ivg | FG5 | Pantothenate synthetase | 6.3.2.1 | 0.459 | |
| 4nes | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.459 | |
| 5hws | NAP | 2-dehydropantoate 2-reductase | / | 0.459 | |
| 3fst | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.458 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.458 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.458 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.458 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.457 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.457 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.456 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.456 | |
| 4xr9 | NAD | CalS8 | / | 0.456 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.455 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.455 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.455 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.454 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.454 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.454 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.454 | |
| 3lb8 | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.454 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.454 | |
| 1c6y | MK1 | Protease | / | 0.453 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.453 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.453 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.453 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.453 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.453 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.453 | |
| 1r6t | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.452 | |
| 1zrq | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.452 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.452 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.452 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.452 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.452 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.451 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.450 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.450 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.450 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.450 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.450 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.450 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.450 | |
| 1msm | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.449 | |
| 3ag6 | PAJ | Pantothenate synthetase | / | 0.449 | |
| 3ieu | GDP | GTPase Era | / | 0.449 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.449 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.449 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3ihk | TPP | Uncharacterized protein | / | 0.448 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.448 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.448 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.447 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.447 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.447 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.447 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.447 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.447 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.447 | |
| 3w2e | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.447 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.446 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.446 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.446 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.446 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.446 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.446 | |
| 4tm3 | FAD | KtzI | / | 0.446 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.445 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.445 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.445 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.445 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.445 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.445 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.445 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.445 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3a3g | DLZ | Lumazine protein | / | 0.445 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.445 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 3r95 | ACO | MccE protein | / | 0.445 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.445 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.445 | |
| 4irn | FAD | AnaB | / | 0.445 | |
| 4p63 | NAD | Probable deoxyhypusine synthase | 2.5.1.46 | 0.445 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1xdp | ATP | Polyphosphate kinase | / | 0.444 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.444 | |
| 2dsg | SAH | Diphthine synthase | / | 0.444 | |
| 2dsh | SAH | Diphthine synthase | / | 0.444 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.444 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.444 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.444 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.444 | |
| 4e2d | FMN | Dehydrogenase | / | 0.444 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.444 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.443 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.443 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1vfr | FMN | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.443 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 2owk | SAH | Diphthine synthase | / | 0.443 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.443 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.443 | |
| 4en4 | ATP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 3bbr | BHY | Glutamate receptor 2 | / | 0.442 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3kgc | LY7 | Glutamate receptor 2 | / | 0.442 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.442 | |
| 3uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.442 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.442 | |
| 4p53 | NAI | 2-epi-5-epi-valiolone synthase | / | 0.442 | |
| 4zse | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.441 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1w5s | ADP | ORC1-type DNA replication protein 2 | / | 0.441 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.441 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.441 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.441 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1b5t | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.440 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.440 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.440 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.440 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.440 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.440 |