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 |
|---|---|---|---|
| 5c3y | AN2 | Ribokinase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5c3y | AN2 | Ribokinase | / | 1.000 | |
| 5c3z | ACP | Ribokinase | / | 0.646 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.589 | |
| 5c41 | ACP | Ribokinase | / | 0.579 | |
| 1lik | ADN | Adenosine kinase | 2.7.1.20 | 0.561 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.561 | |
| 4e8y | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.530 | |
| 3nbv | ANP | Ketohexokinase | / | 0.527 | |
| 3lki | ATP | Fructokinase | / | 0.526 | |
| 3nbw | TR4 | Ketohexokinase | / | 0.493 | |
| 3qai | XNN | Ketohexokinase | / | 0.492 | |
| 3w8q | AGS | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.485 | |
| 3otx | AP5 | Adenosine kinase, putative | / | 0.484 | |
| 3q92 | XNB | Ketohexokinase | / | 0.483 | |
| 1ppj | ANY | Cytochrome b | / | 0.475 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.475 | |
| 4e8w | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.472 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.471 | |
| 3nc9 | TR3 | Ketohexokinase | / | 0.470 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 2oor | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.469 | |
| 1qvr | ANP | Chaperone protein ClpB | / | 0.468 | |
| 2hw1 | ANP | Ketohexokinase | / | 0.468 | |
| 5c40 | ACP | Ribokinase | / | 0.468 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.467 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 2f02 | ATP | Tagatose-6-phosphate kinase | / | 0.464 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.463 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.463 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.463 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.462 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.461 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.461 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.460 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3qa2 | XNA | Ketohexokinase | / | 0.460 | |
| 3wsb | RWZ | Farnesyltransferase, putative | / | 0.460 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.459 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.459 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 1d4j | MSC | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.458 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.458 | |
| 3ofm | 4B0 | Casein kinase II subunit alpha' | 2.7.11.1 | 0.458 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.458 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.458 | |
| 4pd6 | URI | Nucleoside permease | / | 0.458 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.456 | |
| 1rkd | ADP | Ribokinase | / | 0.456 | |
| 1zdw | FLV | Prenyltransferase | / | 0.456 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 3qw4 | U5P | Orotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative | / | 0.456 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.455 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.455 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.455 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.454 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.454 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.454 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.454 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.454 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3ut5 | LOC | Tubulin beta chain | / | 0.454 | |
| 5itz | LOC | Tubulin beta-2B chain | / | 0.454 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.453 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.453 | |
| 3in1 | ADP | Uncharacterized sugar kinase YdjH | 2.7.1 | 0.453 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 3tti | KBI | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.453 | |
| 5a3b | APR | SIR2 family protein | / | 0.453 | |
| 1iy8 | NAD | Levodione reductase | / | 0.452 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.451 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.451 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.451 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.451 | |
| 1k8y | 13P | Tryptophan synthase alpha chain | / | 0.450 | |
| 1onp | FOM | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.450 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 3efw | AK8 | Aurora kinase A | 2.7.11.1 | 0.450 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.450 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.449 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.449 | |
| 3hzi | ATP | Serine/threonine-protein kinase toxin HipA | / | 0.449 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.449 | |
| 3v0t | ATR | Perakine reductase | 1.1.1.317 | 0.449 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.449 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.448 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3cgf | JNF | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.448 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.448 | |
| 3fpj | SAM | Uncharacterized protein | / | 0.448 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.448 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.448 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.447 | |
| 3ics | ADP | Coenzyme A disulfide reductase | / | 0.447 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.447 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.447 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.447 | |
| 4e2d | FMN | Dehydrogenase | / | 0.447 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.446 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.446 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.446 | |
| 2ojj | 82A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.446 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.446 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3cr3 | ADP | PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL | 2.7 | 0.446 | |
| 3ih0 | ANP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.446 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.446 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.446 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.446 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.445 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 4o59 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.445 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.444 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.444 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.444 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.444 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3ruq | ADP | Chaperonin | / | 0.444 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4h3q | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.443 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.443 | |
| 1me8 | RVP | Inosine-5'-monophosphate dehydrogenase | / | 0.443 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.443 | |
| 3d8x | FAD | Thioredoxin reductase 1 | 1.8.1.9 | 0.443 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.443 | |
| 3k5u | PFQ | Aurora kinase A | 2.7.11.1 | 0.443 | |
| 3rus | ADP | Chaperonin | / | 0.443 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.443 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.443 | |
| 4pkh | ADP | Actin, alpha skeletal muscle | / | 0.443 | |
| 5cvf | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.443 | |
| 5dp2 | NAP | CurF | / | 0.443 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.442 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.442 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.442 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.442 | |
| 3u9e | COA | Lmo1369 protein | / | 0.442 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 4fv1 | EK4 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.442 | |
| 4l4x | NDP | AmphI | / | 0.442 | |
| 1kvt | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 2a0c | CK9 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 3gob | HXX | DdmC | / | 0.441 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.441 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.441 | |
| 4lt6 | 3AT | Poly(A) polymerase gamma | 2.7.7.19 | 0.441 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.440 | |
| 3axw | TID | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 | |
| 5ap7 | SVE | Dual specificity protein kinase TTK | 2.7.12.1 | 0.440 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.440 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.440 |