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 |
|---|---|---|---|
| 2gg2 | U12 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2gg2 | U12 | Methionine aminopeptidase | / | 1.000 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.747 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.719 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.667 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.664 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.664 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.662 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.647 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.645 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.639 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.638 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.628 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.622 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.616 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.615 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.601 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.591 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.575 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.570 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.563 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.561 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.560 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.557 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.554 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.550 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.543 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.543 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.540 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.534 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.531 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.527 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.526 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.521 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.520 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.519 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.519 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.517 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.515 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.509 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.509 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.508 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.508 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.507 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.506 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.506 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.506 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.506 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.505 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.502 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.501 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.499 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.498 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.496 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.492 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.492 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.491 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.491 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.489 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.487 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.481 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.477 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.476 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.472 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.471 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.470 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.470 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.470 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.468 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.467 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.466 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.466 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.466 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.466 | |
| 5fmm | MGT | Polymerase basic protein 2 | / | 0.466 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.465 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.463 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.463 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.463 | |
| 4ea2 | RWZ | Dehydrosqualene synthase | / | 0.463 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.462 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.460 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.460 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.459 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.459 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.459 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.457 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.457 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.456 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.456 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.456 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 1v08 | NTZ | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.455 | |
| 3ryk | TYD | dTDP-4-dehydrorhamnose 3,5-epimerase | / | 0.455 | |
| 4g8j | THM | Uridine phosphorylase | / | 0.455 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.452 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.450 | |
| 4q7f | 3D1 | Uncharacterized protein | / | 0.450 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.449 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.449 | |
| 2wvm | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.449 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.449 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.449 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.448 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.447 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.447 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.447 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.447 | |
| 4to0 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.447 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.446 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.445 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.445 | |
| 4rxr | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.445 | |
| 3oe9 | ITD | C-X-C chemokine receptor type 4 | / | 0.445 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.444 | |
| 3zpq | XF5 | Beta-1 adrenergic receptor | / | 0.444 | |
| 4req | 5AD | Methylmalonyl-CoA mutase large subunit | 5.4.99.2 | 0.444 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 2aot | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.443 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.443 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.443 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.442 | |
| 3tdv | GDP | Gentamicin resistance protein | / | 0.442 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 2fjm | 073 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.441 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.441 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3myu | VIB | High affinity transport system protein p37 | / | 0.441 | |
| 3qbj | NXZ | Dipeptidyl peptidase 4 | / | 0.441 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.441 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.441 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.441 | |
| 2a4x | BLM | Mitomycin-binding protein | / | 0.440 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.440 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.440 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.440 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.440 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 5ief | NBV | Neutral alpha-glucosidase AB | 3.2.1.84 | 0.440 |