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 |
|---|---|---|---|
| 5c3y | AN2 | Ribokinase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5c3y | AN2 | Ribokinase | / | 1.000 | |
| 5c3z | ACP | Ribokinase | / | 0.653 | |
| 5c41 | ACP | Ribokinase | / | 0.595 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.571 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.567 | |
| 1gqt | ACP | Ribokinase | / | 0.566 | |
| 1lik | ADN | Adenosine kinase | 2.7.1.20 | 0.556 | |
| 3nbv | ANP | Ketohexokinase | / | 0.553 | |
| 4e8y | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.541 | |
| 3lki | ATP | Fructokinase | / | 0.534 | |
| 3otx | AP5 | Adenosine kinase, putative | / | 0.497 | |
| 3q92 | XNB | Ketohexokinase | / | 0.497 | |
| 3qai | XNN | Ketohexokinase | / | 0.497 | |
| 3w8q | AGS | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.495 | |
| 3nbw | TR4 | Ketohexokinase | / | 0.493 | |
| 1ppj | ANY | Cytochrome b | / | 0.482 | |
| 2hw1 | ANP | Ketohexokinase | / | 0.481 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.480 | |
| 3umo | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.477 | |
| 5c40 | ACP | Ribokinase | / | 0.477 | |
| 1qvr | ANP | Chaperone protein ClpB | / | 0.476 | |
| 2f02 | ATP | Tagatose-6-phosphate kinase | / | 0.474 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.471 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.469 | |
| 4a0m | NAD | Betaine aldehyde dehydrogenase, chloroplastic | 1.2.1.8 | 0.469 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.469 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.467 | |
| 4e8w | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.466 | |
| 1d4j | MSC | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.465 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.465 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.465 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 1pn3 | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.464 | |
| 1rkd | ADP | Ribokinase | / | 0.464 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.464 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.463 | |
| 2j9l | ATP | H(+)/Cl(-) exchange transporter 5 | / | 0.462 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.462 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 3in1 | ADP | Uncharacterized sugar kinase YdjH | 2.7.1 | 0.462 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.462 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.461 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.461 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.461 | |
| 3hzi | ATP | Serine/threonine-protein kinase toxin HipA | / | 0.461 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.461 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.460 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.460 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.460 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.460 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.459 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.459 | |
| 5cvf | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.459 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.458 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.458 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.458 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.458 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.457 | |
| 3keu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.457 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.457 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.457 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.456 | |
| 3nc9 | TR3 | Ketohexokinase | / | 0.456 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.456 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.456 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.455 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.455 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.455 | |
| 3d8x | FAD | Thioredoxin reductase 1 | 1.8.1.9 | 0.455 | |
| 3ih0 | ANP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.455 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.455 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.455 | |
| 1iy8 | NAD | Levodione reductase | / | 0.454 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.454 | |
| 3bgb | LJG | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.454 | |
| 4h3q | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.454 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.453 | |
| 3qa2 | XNA | Ketohexokinase | / | 0.453 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.452 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.452 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.452 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.452 | |
| 2d4v | NAD | Isocitrate dehydrogenase [NADP] | / | 0.451 | |
| 2fhj | MFN | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.451 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.451 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3h0a | D30 | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 3rus | ADP | Chaperonin | / | 0.451 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.451 | |
| 4eud | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.451 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.451 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 2vxo | XMP | GMP synthase [glutamine-hydrolyzing] | 6.3.5.2 | 0.450 | |
| 5a3c | NAD | SIR2 family protein | / | 0.450 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.449 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.449 | |
| 2qn7 | HBZ | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.449 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.449 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.449 | |
| 4gdd | FAD | UDP-galactopyranose mutase | / | 0.449 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.449 | |
| 5a3b | APR | SIR2 family protein | / | 0.449 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1d4h | BEH | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 1ig1 | ANP | Death-associated protein kinase 1 | 2.7.11.1 | 0.448 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.448 | |
| 2voj | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.448 | |
| 3uqd | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.448 | |
| 1ha3 | MAU | Elongation factor Tu-A | / | 0.447 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.447 | |
| 2onm | ADP | Aldehyde dehydrogenase, mitochondrial | 1.2.1.3 | 0.447 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 3ruq | ADP | Chaperonin | / | 0.447 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.447 | |
| 4anm | WUL | Casein kinase II subunit alpha | 2.7.11.1 | 0.447 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.447 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.447 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.446 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.446 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.446 | |
| 1qvn | FRI | Interleukin-2 | / | 0.446 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.446 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.446 | |
| 2ehu | NAD | 1-pyrroline-5-carboxylate dehydrogenase | / | 0.446 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.446 | |
| 2x19 | GTP | GTP-binding nuclear protein GSP1/CNR1 | / | 0.446 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.446 | |
| 3fpj | SAM | Uncharacterized protein | / | 0.446 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.446 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.446 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.446 | |
| 3zuy | TCH | Transporter | / | 0.446 | |
| 4irn | FAD | AnaB | / | 0.446 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.446 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.446 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.446 | |
| 4xf7 | ACP | Carbohydrate/pyrimidine kinase, PfkB family | / | 0.446 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.445 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 2dcn | ADP | 2-keto-3-deoxy-gluconate kinase | / | 0.445 | |
| 2p2b | PRX | Acetyl-coenzyme A synthetase | / | 0.445 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.445 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.445 | |
| 5ap7 | SVE | Dual specificity protein kinase TTK | 2.7.12.1 | 0.445 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.444 | |
| 2h8h | H8H | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.444 | |
| 2ojj | 82A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.444 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.444 | |
| 5hws | NAP | 2-dehydropantoate 2-reductase | / | 0.444 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.443 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.443 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.443 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.443 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.443 | |
| 2cdu | FAD | NADH oxidase | / | 0.443 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.443 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.443 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.443 | |
| 3suf | SUE | Polyprotein | / | 0.443 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.443 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.443 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.443 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2ab8 | ACP | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.442 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.442 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.442 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.441 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.441 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.441 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.441 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 4fr4 | STU | Serine/threonine-protein kinase 32A | 2.7.11.1 | 0.441 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.441 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.441 | |
| 4ydu | ADP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.441 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.440 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2uzt | SS3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3g7j | GTX | Glutathione transferase GST1-4 | / | 0.440 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.440 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.440 | |
| 3nu6 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 4bwx | AGS | PAB-dependent poly(A)-specific ribonuclease subunit pan3 | / | 0.440 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.440 |