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 |
|---|---|---|---|
| 4tla | ADP | Circadian clock protein kinase KaiC | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4tla | ADP | Circadian clock protein kinase KaiC | 2.7.11.1 | 1.000 | |
| 4tlb | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.636 | |
| 4tlc | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.631 | |
| 2gbl | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.619 | |
| 3s1a | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.617 | |
| 4tl7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.616 | |
| 3k0f | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.614 | |
| 4tl9 | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.606 | |
| 3jzm | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.596 | |
| 1u9i | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.582 | |
| 1tf7 | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.581 | |
| 4tld | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.578 | |
| 4tle | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.575 | |
| 3dvl | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.572 | |
| 4o0m | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.559 | |
| 4tl6 | ANP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.558 | |
| 4tl8 | AGS | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.552 | |
| 3k0a | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.502 | |
| 2dr3 | ADP | UPF0273 protein PH0284 | / | 0.500 | |
| 2zts | ADP | Uncharacterized protein | / | 0.485 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.474 | |
| 3b03 | VNR | Isopentenyl-diphosphate delta-isomerase | / | 0.473 | |
| 5dp2 | NAP | CurF | / | 0.472 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.471 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.470 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.468 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.464 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.463 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.461 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.461 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.461 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.460 | |
| 2p5f | SAH | Diphthine synthase | / | 0.459 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.459 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.458 | |
| 2owk | SAH | Diphthine synthase | / | 0.458 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.458 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 2e16 | SAH | Diphthine synthase | / | 0.457 | |
| 2ejz | SAH | Diphthine synthase | / | 0.455 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.455 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.455 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.455 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.455 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.455 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.454 | |
| 2dsh | SAH | Diphthine synthase | / | 0.454 | |
| 2f6r | ACO | Bifunctional coenzyme A synthase | / | 0.454 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.453 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.453 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.452 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.452 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.452 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.452 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.452 | |
| 1het | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.451 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.451 | |
| 4kqr | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.451 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3bbf | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.450 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.450 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.450 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.450 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1osv | CHC | Bile acid receptor | / | 0.449 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.449 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.449 | |
| 5kjf | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.448 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 2p5c | SAH | Diphthine synthase | / | 0.448 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.448 | |
| 4u07 | ATP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.448 | |
| 5a3b | APR | SIR2 family protein | / | 0.448 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.447 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.447 | |
| 1vce | SAH | Diphthine synthase | / | 0.447 | |
| 2dek | SAH | Diphthine synthase | / | 0.447 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.447 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.447 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.447 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.446 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 3ipu | O40 | Oxysterols receptor LXR-alpha | / | 0.446 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.446 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.446 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.445 | |
| 2owu | SAH | Diphthine synthase | / | 0.445 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.445 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.445 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.445 | |
| 4jln | 18V | Deoxycytidine kinase | 2.7.1.74 | 0.445 | |
| 4kqq | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.445 | |
| 4xxv | NAD | 3-isopropylmalate dehydrogenase | / | 0.445 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.444 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 2pck | SAH | Diphthine synthase | / | 0.444 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.444 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.444 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4dwv | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.443 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.443 | |
| 2p6i | SAH | Diphthine synthase | / | 0.443 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.443 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.443 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.443 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.443 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.442 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.442 | |
| 2e4n | SAH | Diphthine synthase | / | 0.442 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.442 | |
| 3hek | BD0 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 2ehl | SAH | Diphthine synthase | / | 0.441 | |
| 2fvl | NAP | Aldo-keto reductase family 1 member C4 | 1.1.1.225 | 0.441 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.441 | |
| 2hut | SAH | Diphthine synthase | / | 0.441 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.441 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.441 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 5cdt | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 5kcp | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.440 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.440 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.440 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.440 | |
| 4dxh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.440 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.440 |