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 |
|---|---|---|---|
| 2gg3 | U13 | Methionine aminopeptidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2gg3 | U13 | Methionine aminopeptidase | / | 1.000 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.681 | |
| 2gg8 | U15 | Methionine aminopeptidase | / | 0.667 | |
| 2gg0 | U11 | Methionine aminopeptidase | / | 0.665 | |
| 2ggb | U17 | Methionine aminopeptidase | / | 0.635 | |
| 2p98 | YE7 | Methionine aminopeptidase | / | 0.631 | |
| 3d27 | W29 | Methionine aminopeptidase | / | 0.631 | |
| 2q92 | B23 | Methionine aminopeptidase | / | 0.628 | |
| 2q96 | A18 | Methionine aminopeptidase | / | 0.628 | |
| 2gg2 | U12 | Methionine aminopeptidase | / | 0.617 | |
| 3iu8 | T03 | Methionine aminopeptidase 2 | / | 0.615 | |
| 2q94 | A04 | Methionine aminopeptidase | / | 0.612 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.607 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.602 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.595 | |
| 1c23 | MPH | Methionine aminopeptidase | / | 0.584 | |
| 4iku | SHX | Methionine aminopeptidase 1 | / | 0.580 | |
| 2g6p | HM2 | Methionine aminopeptidase 1 | / | 0.579 | |
| 2evm | FC2 | Methionine aminopeptidase | / | 0.578 | |
| 2gg9 | U16 | Methionine aminopeptidase | / | 0.576 | |
| 4ikt | TFV | Methionine aminopeptidase 1 | / | 0.576 | |
| 2q93 | B21 | Methionine aminopeptidase | / | 0.575 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.575 | |
| 2evc | FC3 | Methionine aminopeptidase | / | 0.574 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.565 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.554 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.552 | |
| 4ikr | PVP | Methionine aminopeptidase 1 | / | 0.551 | |
| 4fli | Y16 | Methionine aminopeptidase 1 | / | 0.550 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.544 | |
| 4flj | Y08 | Methionine aminopeptidase 1 | / | 0.535 | |
| 4hxx | 1AY | Methionine aminopeptidase 1 | / | 0.535 | |
| 3iu9 | T07 | Methionine aminopeptidase 2 | / | 0.534 | |
| 1xnz | FCD | Methionine aminopeptidase | / | 0.531 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.529 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.525 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.516 | |
| 3pkc | Y08 | Methionine aminopeptidase 2 | / | 0.514 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.510 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.509 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.504 | |
| 1qzy | TDE | Methionine aminopeptidase 2 | / | 0.503 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.502 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.499 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.498 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.497 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.495 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.494 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.493 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.493 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.489 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.489 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.486 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.485 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.485 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.483 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.481 | |
| 4q7f | 3D1 | Uncharacterized protein | / | 0.480 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.479 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.478 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.477 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.476 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.473 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.473 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.470 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.470 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.470 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.469 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.468 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.467 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.466 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.466 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.465 | |
| 4rxr | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.465 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.464 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.463 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.460 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.460 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.460 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.460 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.460 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.459 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.458 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.458 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.458 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.457 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.455 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.455 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.455 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.453 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.453 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.453 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.453 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.452 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 3mo0 | SAH | Histone-lysine N-methyltransferase EHMT1 | / | 0.452 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.452 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2x91 | LPR | Angiotensin-converting enzyme | 3.4.15.1 | 0.451 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.451 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.451 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.451 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.450 | |
| 2jgb | MGT | Eukaryotic translation initiation factor 4E type 2 | / | 0.450 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4r5w | XAV | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.450 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.449 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.449 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.449 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.448 | |
| 4xcz | T3Q | Qdtf | / | 0.448 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 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 | 0.447 | |
| 2get | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.447 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.446 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.446 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.446 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.446 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4phl | PIL | Phosphodiesterase | / | 0.446 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.445 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2v9c | MRE | FMN-dependent NADH-azoreductase 1 | / | 0.445 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.445 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.444 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.444 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.444 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.443 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.443 | |
| 3arp | DEQ | Chitinase A | / | 0.443 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.443 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 1esm | COA | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.442 | |
| 2xwe | AMF | Glucosylceramidase | 3.2.1.45 | 0.442 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.442 | |
| 1vhz | APR | ADP compounds hydrolase NudE | 3.6.1 | 0.441 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.441 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2jl1 | NAP | Triphenylmethane reductase | / | 0.441 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.441 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2x92 | X92 | Angiotensin-converting enzyme | 3.4.15.1 | 0.440 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.440 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.440 |