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 |
|---|---|---|---|
| 2p99 | YE6 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2p99 | YE6 | Methionine aminopeptidase | / | 1.000 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.721 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.699 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.674 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.670 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.664 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.621 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.608 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.607 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.604 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.604 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.595 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.594 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.586 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.581 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.578 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.576 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.575 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.567 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.566 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.563 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.559 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.555 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.552 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.550 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.540 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.535 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.534 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.531 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.529 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.526 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.521 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.515 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.508 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.503 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.502 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.499 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.497 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.488 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.484 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.481 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.479 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.477 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.476 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.474 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.473 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.473 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.470 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.470 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 4rxr | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.469 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.468 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.468 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.467 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.466 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.466 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.465 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.463 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.462 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.460 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.459 | |
| 1opm | IYG | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.458 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.458 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.458 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.457 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 2r8p | T6F | Transketolase 1 | / | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.455 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.454 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.452 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.451 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.450 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.450 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.450 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.450 | |
| 2r8o | T5X | Transketolase 1 | / | 0.450 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.449 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.449 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.449 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.448 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.448 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.448 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.447 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.447 | |
| 1tkc | M6T | Transketolase 1 | 2.2.1.1 | 0.447 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.447 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.447 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.446 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.446 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.445 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.445 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4jic | FMN | GTN Reductase | / | 0.445 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.444 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.443 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.443 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3tqc | ADP | Pantothenate kinase | / | 0.442 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4lh7 | 1X8 | DNA ligase | / | 0.442 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.441 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.441 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.441 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.441 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.441 | |
| 1dgg | NDP | Catalase | 1.11.1.6 | 0.440 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.440 | |
| 1xr2 | C2F | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | 2.1.1.14 | 0.440 | |
| 2r5n | TPP | Transketolase 1 | / | 0.440 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.440 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.440 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.440 | |
| 4e2y | JHZ | Methyltransferase | / | 0.440 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.440 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.440 | |
| 4kxj | P34 | Nucleoprotein | / | 0.440 | |
| 4to3 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.440 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.440 |