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 |
|---|---|---|---|
| 4jwj | SAH | tRNA (guanine(9)-N1)-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4jwj | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 1.000 | |
| 4jwh | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.568 | |
| 4jwf | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.521 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.517 | |
| 4yvh | SFG | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.487 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.472 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.471 | |
| 2yy8 | MTA | tRNA (cytidine(56)-2'-O)-methyltransferase | / | 0.468 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.468 | |
| 4h4y | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.468 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.467 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.467 | |
| 1p9p | SAH | tRNA (guanine-N(1)-)-methyltransferase | / | 0.465 | |
| 4yvg | SAM | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.465 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.464 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.464 | |
| 4i9h | 1E4 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.464 | |
| 1l4l | NCN | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.463 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.463 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.462 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.462 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.461 | |
| 1rx5 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2ewv | ADP | Twitching motility protein PilT | / | 0.459 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.459 | |
| 2yy8 | SAM | tRNA (cytidine(56)-2'-O)-methyltransferase | / | 0.459 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.459 | |
| 1uak | SAM | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.458 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.458 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.458 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.458 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.457 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.457 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 3w23 | 3RO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.456 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.455 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.454 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.454 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.454 | |
| 1iy8 | NAD | Levodione reductase | / | 0.453 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.453 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.453 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.453 | |
| 1tww | HH2 | Dihydropteroate synthase | / | 0.452 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.452 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.452 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.452 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.452 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.452 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.451 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.451 | |
| 3n4k | SAH | tRNA (cytidine(34)-2'-O)-methyltransferase | / | 0.451 | |
| 3o0o | 5AD | Vitamin B12-dependent ribonucleotide reductase | / | 0.451 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.451 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 4mk0 | 29X | Beta-adrenergic receptor kinase 1 | 2.7.11.15 | 0.451 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.450 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.450 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.450 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.450 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.450 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase | / | 0.449 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.449 | |
| 3u2m | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.449 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.449 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.449 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.449 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.448 | |
| 1ra3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2bfr | ADP | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.448 | |
| 2cgu | 3A3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.448 | |
| 4a6b | QG8 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4r9u | ANP | Vitamin B12 import ATP-binding protein BtuD | / | 0.448 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1l4m | NCN | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.447 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.447 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.447 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.447 | |
| 3bbd | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 0.447 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.447 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.446 | |
| 2qn7 | HBZ | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.446 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.446 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.445 | |
| 3zl8 | ADP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.445 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.445 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.445 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1mei | MOA | Inosine-5'-monophosphate dehydrogenase | / | 0.444 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.444 | |
| 2f7z | 6EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2owu | SAH | Diphthine synthase | / | 0.444 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.444 | |
| 3d2m | COA | Amino-acid acetyltransferase | / | 0.444 | |
| 4gkm | 683 | Anthranilate phosphoribosyltransferase | / | 0.444 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.444 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.443 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1rx4 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2aqj | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.443 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.443 | |
| 4ple | CPS | Nuclear receptor subfamily 5 group A member 2 | / | 0.443 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.443 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2c3l | IDZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2ele | SAH | Diphthine synthase | / | 0.442 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.442 | |
| 2owk | SAH | Diphthine synthase | / | 0.442 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 3w3o | ROE | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.442 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.442 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 5l3s | GNP | Signal recognition particle receptor FtsY | / | 0.442 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.441 | |
| 2c1a | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2egl | SAH | Diphthine synthase | / | 0.441 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.441 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.441 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.441 | |
| 3eql | MXP | DNA-directed RNA polymerase subunit beta | / | 0.441 | |
| 3eql | MXP | DNA-directed RNA polymerase subunit beta' | / | 0.441 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.441 | |
| 3nk7 | SAM | 23S rRNA (adenosine(1067)-2'-O)-methyltransferase | / | 0.441 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4btu | 6XS | Coagulation factor X | 3.4.21.6 | 0.441 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.441 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 5a3b | APR | SIR2 family protein | / | 0.441 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.441 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.440 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.440 | |
| 2d0k | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.440 | |
| 2uw4 | L15 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.440 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.440 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.440 |