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 |
|---|---|---|---|
| 1r58 | AO5 | Methionine aminopeptidase 2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 1.000 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.735 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.697 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.687 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.685 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.684 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.670 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.659 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.647 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.624 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.613 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.516 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.504 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.498 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.497 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.495 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.495 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.492 | |
| 1zg3 | 2HI | Isoflavone 4'-O-methyltransferase | / | 0.486 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.486 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.483 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.483 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.482 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.481 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.481 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.477 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.477 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.475 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.474 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.472 | |
| 2bxo | OPB | Serum albumin | / | 0.471 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.471 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.470 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.469 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.467 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.467 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.467 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.467 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.466 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.464 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.463 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.462 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.461 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.461 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.461 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.461 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.460 | |
| 4phl | PIL | Phosphodiesterase | / | 0.460 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 0.459 | |
| 1fkl | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.458 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.458 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.458 | |
| 1h69 | ARH | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.457 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.457 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.457 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.457 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.456 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.456 | |
| 4dh0 | MR8 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.456 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.456 | |
| 2vd7 | PD2 | Lysine-specific demethylase 4A | 1.14.11 | 0.455 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1fxf | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.454 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.454 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.454 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.454 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.454 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.454 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.454 | |
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.453 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.453 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.453 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.452 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.452 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.452 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.452 | |
| 3abx | RCB | Glucanase | / | 0.451 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 3frk | TQP | QdtB | / | 0.451 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.450 | |
| 2rds | 1PL | 1-deoxypentalenic acid 11-beta-hydroxylase | 1.14.11.35 | 0.450 | |
| 3c1o | NAP | Eugenol synthase | / | 0.450 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.450 | |
| 3s8x | E59 | Carbonic anhydrase 2 | 4.2.1.1 | 0.450 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.450 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.449 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.449 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.449 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 3zhu | TD8 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.449 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.449 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.449 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.448 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1fkb | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.447 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.447 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.447 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.447 | |
| 4h9t | HL4 | Phosphotriesterase | / | 0.447 | |
| 1ddt | APU | Diphtheria toxin | / | 0.446 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.446 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.446 | |
| 1xq0 | 4TR | Carbonic anhydrase 2 | 4.2.1.1 | 0.445 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.445 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3b4f | TUO | Carbonic anhydrase 2 | 4.2.1.1 | 0.445 | |
| 3k4s | 0MO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.445 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.445 | |
| 1aqu | EST | Estrogen sulfotransferase, testis isoform | 2.8.2.4 | 0.444 | |
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.444 | |
| 1jed | ADP | Sulfate adenylyltransferase | / | 0.444 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.444 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.444 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.444 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ydd | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.444 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4tkg | 09L | Tankyrase-2 | 2.4.2.30 | 0.444 | |
| 1h35 | R01 | Squalene--hopene cyclase | 4.2.1.129 | 0.443 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2b3v | ACO | Diamine acetyltransferase 1 | / | 0.443 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.443 | |
| 3zgz | 84T | Leucine--tRNA ligase | / | 0.443 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.443 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.442 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1s4p | GDP | Glycolipid 2-alpha-mannosyltransferase | / | 0.441 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3int | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.441 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 4iae | 1DX | Alr2278 protein | / | 0.441 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.440 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |