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 |
|---|---|---|---|
| 4lcn | GNG | Cytidine and deoxycytidylate deaminase zinc-binding region |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4lcn | GNG | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 1.000 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.529 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.527 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.524 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.521 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.512 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.508 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.507 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.495 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.494 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.493 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.492 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.490 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.489 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.488 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.485 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.480 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.480 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.480 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.478 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.477 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.476 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.476 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.474 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.473 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 4gv7 | MEW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.472 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.471 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.471 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.471 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.470 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.470 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.469 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.468 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.468 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.468 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.467 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.466 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.466 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.466 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.465 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.465 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.465 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.465 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.464 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.464 | |
| 4ld2 | CTN | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 0.464 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.463 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.463 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.462 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 1gm9 | SOX | Penicillin G acylase | 3.5.1.11 | 0.460 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.460 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.460 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.460 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.460 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.460 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.460 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.459 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.459 | |
| 2vet | UMP | Thymidylate synthase | / | 0.459 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 1xq0 | 4TR | Carbonic anhydrase 2 | 4.2.1.1 | 0.457 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 1m9h | NAD | 2,5-diketo-D-gluconic acid reductase A | 1.1.1.346 | 0.456 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.456 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.456 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.454 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.454 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.453 | |
| 2pb1 | NFG | Glucan 1,3-beta-glucosidase | / | 0.453 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.453 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.453 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.453 | |
| 1by5 | GLY_GLY_GLY_AHO_AHO_AHO_FE | Ferrichrome-iron receptor | / | 0.452 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.452 | |
| 2dv0 | ZST | Aldose reductase | 1.1.1.21 | 0.452 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.452 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.452 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.452 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.451 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3nhp | HGZ | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.451 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.451 | |
| 1ddt | APU | Diphtheria toxin | / | 0.450 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 3ny9 | JSZ | Beta-2 adrenergic receptor | / | 0.450 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.449 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.449 | |
| 1uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.448 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.448 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.448 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.448 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1lke | DOG | Bilin-binding protein | / | 0.447 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.447 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.447 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.447 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.447 | |
| 3br9 | DEY | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.447 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.447 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.446 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.446 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.446 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.446 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.446 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1v48 | HA1 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.445 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.445 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.445 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4hcy | 0YN | Transketolase | / | 0.445 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.444 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4j7g | TRH | PCZA361.3 | / | 0.444 | |
| 4rxr | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.443 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.443 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.443 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.443 | |
| 2nq7 | HM5 | Methionine aminopeptidase 1 | / | 0.443 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3e78 | TPP | High affinity transport system protein p37 | / | 0.443 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4e32 | DWN | Methyltransferase | / | 0.443 | |
| 5dp2 | NAP | CurF | / | 0.443 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2idv | M7G | Eukaryotic translation initiation factor 4E-1 | / | 0.442 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.442 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.442 | |
| 3v2u | ATP | Protein GAL3 | / | 0.442 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4hrq | AZG | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 0.442 | |
| 4jt9 | 1NS | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.442 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.442 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2r59 | PH0 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.441 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.441 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.441 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.441 | |
| 5a8e | XTK | Beta-1 adrenergic receptor | / | 0.441 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.440 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.440 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.440 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.440 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.440 |