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 |
|---|---|---|---|
| 1lmc | BUL | Lysozyme C II | 3.2.1.17 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1lmc | BUL | Lysozyme C II | 3.2.1.17 | 1.000 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.491 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.490 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.482 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.481 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.479 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.477 | |
| 2iml | FMN | Uncharacterized protein | / | 0.475 | |
| 4a6e | ASE | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.474 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 1h65 | GDP | Translocase of chloroplast 34 | 3.6.5 | 0.471 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.470 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.469 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.469 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.466 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.466 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.465 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.465 | |
| 4ise | 1FW | Glucokinase | 2.7.1.2 | 0.465 | |
| 2d1s | SLU | Luciferin 4-monooxygenase | 1.13.12.7 | 0.464 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.463 | |
| 3a20 | FMN | FMN-binding protein | / | 0.463 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.463 | |
| 4do3 | 0LA | Fatty-acid amide hydrolase 1 | 3.5.1.99 | 0.463 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.461 | |
| 4pkw | GM6 | Lethal factor | 3.4.24.83 | 0.461 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3fnf | JPM | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 3qbw | ADP | Anhydro-N-acetylmuramic acid kinase | / | 0.460 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.459 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.459 | |
| 1g8o | U5P | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.458 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.458 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.458 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.457 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.457 | |
| 3jzi | JZL | Biotin carboxylase | 6.3.4.14 | 0.457 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.455 | |
| 2egs | SAH | Diphthine synthase | / | 0.455 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 1mv8 | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.454 | |
| 1ppj | ANY | Cytochrome b | / | 0.454 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.454 | |
| 1u2g | APR | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.453 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.453 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.453 | |
| 2egb | SAH | Diphthine synthase | / | 0.452 | |
| 3cb2 | GDP | Tubulin gamma-1 chain | / | 0.452 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 1gaw | FAD | Ferredoxin | / | 0.451 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.451 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.451 | |
| 2yj4 | ATP | Copper-transporting ATPase | / | 0.451 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.450 | |
| 2nr4 | FMN | Conserved protein | / | 0.450 | |
| 2pau | D5M | 5'-deoxynucleotidase YfbR | / | 0.450 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.450 | |
| 2zre | AGS | Protein RecA | / | 0.450 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.450 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.450 | |
| 3psy | RB9 | Endothiapepsin | 3.4.23.22 | 0.449 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.448 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.448 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.448 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.448 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.448 | |
| 3czr | 3CZ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 4jyz | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.448 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.446 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2pcg | SAH | Diphthine synthase | / | 0.446 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.446 | |
| 1b3r | NAD | Adenosylhomocysteinase | 3.3.1.1 | 0.445 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1xag | NAD | 3-dehydroquinate synthase | / | 0.445 | |
| 2owf | SAH | Diphthine synthase | / | 0.445 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.445 | |
| 3ox3 | 4X4 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.445 | |
| 3zm6 | 2GN | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.445 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.445 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.445 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.444 | |
| 1tcw | IM1 | Gag-Pol polyprotein | / | 0.444 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.444 | |
| 2dsg | SAH | Diphthine synthase | / | 0.444 | |
| 2emu | SAH | Diphthine synthase | / | 0.444 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.444 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.444 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.444 | |
| 3ntd | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.444 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.444 | |
| 1c7o | PPG | Hemolysin | / | 0.443 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.443 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.443 | |
| 2el3 | SAH | Diphthine synthase | / | 0.443 | |
| 2toh | HBI | Tyrosine 3-monooxygenase | 1.14.16.2 | 0.443 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4hdp | G52 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.442 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1xaj | NAD | 3-dehydroquinate synthase | / | 0.442 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.442 | |
| 2bif | ANP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 | 2.7.1.105 | 0.442 | |
| 2ele | SAH | Diphthine synthase | / | 0.442 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.442 | |
| 2vag | V25 | Dual specificity protein kinase CLK1 | 2.7.12.1 | 0.442 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.442 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.442 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.442 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.442 | |
| 5jjr | SAH | Genome polyprotein | / | 0.442 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 1zdw | FLV | Prenyltransferase | / | 0.441 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.441 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3abi | NAD | Uncharacterized protein | / | 0.441 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.441 | |
| 3lth | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.441 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.441 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 4dl9 | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.441 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.441 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.440 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 2eld | SAH | Diphthine synthase | / | 0.440 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.440 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.440 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2rl1 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.440 | |
| 2vk8 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.440 | |
| 3kwn | 23Z | Cathepsin S | 3.4.22.27 | 0.440 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.440 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |