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 |
|---|---|---|---|
| 3nju | ANN | Acidic phospholipase A2 3 | 3.1.1.4 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3nju | ANN | Acidic phospholipase A2 3 | 3.1.1.4 | 1.000 | |
| 1db4 | 8IN | Phospholipase A2, membrane associated | / | 0.515 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.514 | |
| 3up0 | D7S | aceDAF-12 | / | 0.500 | |
| 2b96 | ANN | Phospholipase A2 | 3.1.1.4 | 0.499 | |
| 3ix3 | OHN | Transcriptional activator protein LasR | / | 0.493 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.481 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.480 | |
| 1s07 | PLP | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.479 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.477 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.474 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.473 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.473 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.472 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.471 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.469 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 3eld | SFG | Methyltransferase | / | 0.468 | |
| 2uv0 | OHN | Transcriptional activator protein LasR | / | 0.467 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.467 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.465 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.465 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.465 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.464 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.464 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.464 | |
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.464 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.463 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.462 | |
| 1dcy | I3N | Phospholipase A2, membrane associated | / | 0.461 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.461 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.461 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.461 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.460 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.460 | |
| 4jxr | ACO | Acetyltransferase | / | 0.460 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.459 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 3eku | CY9 | Actin-5C | / | 0.459 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.459 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.457 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.457 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.457 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.457 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.457 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.456 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.456 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.456 | |
| 1rd4 | L08 | Integrin alpha-L | / | 0.455 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.455 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.455 | |
| 2oli | IOP | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.455 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.455 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.455 | |
| 4e2x | SAH | Methyltransferase | / | 0.455 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.454 | |
| 2uyw | BTN | Avd protein | / | 0.454 | |
| 3c3e | GDP | 2-phospho-L-lactate transferase | / | 0.454 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.454 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.454 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.454 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.454 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.453 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.453 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.453 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.453 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.452 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.452 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.452 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.452 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.451 | |
| 3i5x | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.451 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.451 | |
| 1db5 | 6IN | Phospholipase A2, membrane associated | / | 0.450 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.450 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.450 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3inv | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 3x2f | NAI | Adenosylhomocysteinase | / | 0.450 | |
| 4kc4 | WS3 | Histo-blood group ABO system transferase | / | 0.450 | |
| 4x5j | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.449 | |
| 2fxu | BID | Actin, alpha skeletal muscle | / | 0.449 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 4e31 | JHZ | Methyltransferase | / | 0.448 | |
| 3bgx | TMP | Thymidylate synthase | / | 0.447 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4qer | STL | Phospholipase A2 VRV-PL-VIIIa | / | 0.447 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.446 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.446 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.446 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.446 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.446 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.446 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 5dp2 | NAP | CurF | / | 0.446 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.446 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.446 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.445 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3pft | FMN | Flavin reductase | / | 0.445 | |
| 3x2w | ATP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 4n1g | CEI | Obelin | / | 0.445 | |
| 4y4j | LNR | Endothiapepsin | 3.4.23.22 | 0.445 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.444 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2q3e | NAI | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.444 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.444 | |
| 3ely | SAH | Methyltransferase | / | 0.444 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 3pll | F06 | Endothiapepsin | 3.4.23.22 | 0.444 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 5l3d | FAD | Lysine-specific histone demethylase 1A | 1 | 0.444 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.443 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.443 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.443 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.443 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.443 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.443 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.443 | |
| 4x5h | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 2cje | DUN | DUTPase | / | 0.442 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3a0t | ADP | Sensor histidine kinase | / | 0.442 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.442 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 4l4x | NDP | AmphI | / | 0.442 | |
| 4y3q | F02 | Endothiapepsin | 3.4.23.22 | 0.442 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.442 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.441 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2abj | PLP | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.441 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.441 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.441 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.441 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3ha3 | SAH | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.441 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.441 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.441 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.441 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4gtp | 7TP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.441 | |
| 2bju | IH4 | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.440 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.440 | |
| 4cf1 | IY7 | Integrase | / | 0.440 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 5b0o | ADP | Flagellum-specific ATP synthase | 3.6.3.14 | 0.440 |