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 |
|---|---|---|---|
| 2q96 | A18 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2q96 | A18 | Methionine aminopeptidase | / | 1.000 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.797 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.702 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.683 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.674 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.651 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.632 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.631 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.630 | |
| 2gg3 | U13 | Methionine aminopeptidase | / | 0.613 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.608 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.605 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.601 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.600 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.598 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.576 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.573 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.554 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.552 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.551 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.547 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.542 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.537 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.537 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.529 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.524 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.524 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.517 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.514 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.506 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.503 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.502 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.498 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.496 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.488 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.487 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.487 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.484 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.480 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.477 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.477 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.474 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.474 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.474 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.473 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.468 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 3arp | DEQ | Chitinase A | / | 0.468 | |
| 1ld8 | U49 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.467 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.467 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.467 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.466 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.466 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.464 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.464 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.464 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 2vd7 | PD2 | Lysine-specific demethylase 4A | 1.14.11 | 0.462 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.461 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.461 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.461 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.459 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.459 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4q7f | 3D1 | Uncharacterized protein | / | 0.459 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.458 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.458 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.457 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.457 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.457 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.456 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.456 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.456 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.456 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.455 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.455 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.455 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.454 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.454 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.454 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.453 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.453 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.452 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.452 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.450 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.450 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.450 | |
| 3mo0 | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.450 | |
| 3ryk | TYD | dTDP-4-dehydrorhamnose 3,5-epimerase | / | 0.450 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.450 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.449 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.449 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.449 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.448 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.448 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.448 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.448 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.448 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 3qbj | NXZ | Dipeptidyl peptidase 4 | / | 0.448 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.448 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.448 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.447 | |
| 2x91 | LPR | Angiotensin-converting enzyme | 3.4.15.1 | 0.447 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.447 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.446 | |
| 2v9c | MRE | FMN-dependent NADH-azoreductase 1 | / | 0.446 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.446 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.446 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4xcz | T3Q | Qdtf | / | 0.446 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.445 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.445 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.445 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.445 | |
| 1nl4 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.444 | |
| 1vf3 | GDN | Glutathione S-transferase 3 | 2.5.1.18 | 0.444 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.444 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.444 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.444 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1iki | REY | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.443 | |
| 2bxo | OPB | Serum albumin | / | 0.443 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.443 | |
| 2x95 | X95 | Angiotensin-converting enzyme | 3.4.15.1 | 0.443 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1oyn | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.442 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.441 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 4lxl | PD2 | Lysine-specific demethylase 4B | 1.14.11 | 0.441 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.440 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.440 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.440 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.440 | |
| 3g5i | DNB | Pyrimidine-specific ribonucleoside hydrolase RihA | / | 0.440 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 |