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 |
|---|---|---|---|
| 4cb5 | 93G | Polymerase basic protein 2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4cb5 | 93G | Polymerase basic protein 2 | / | 1.000 | |
| 4cb4 | MGT | Polymerase basic protein 2 | / | 0.578 | |
| 4cb6 | 29R | Polymerase basic protein 2 | / | 0.576 | |
| 2vqz | MGT | Polymerase basic protein 2 | / | 0.555 | |
| 4eqk | MGT | Polymerase basic protein 2 | / | 0.549 | |
| 5fmm | MGT | Polymerase basic protein 2 | / | 0.549 | |
| 4nce | MGT | Polymerase basic protein 2 | / | 0.543 | |
| 4cb7 | 41G | Polymerase basic protein 2 | / | 0.537 | |
| 3fvu | IAC | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.520 | |
| 4es5 | MGT | Polymerase basic protein 2 | / | 0.513 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.507 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.495 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.495 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.493 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.492 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.491 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.490 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.490 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.488 | |
| 2aj8 | SC3 | Dipeptidyl peptidase 4 | / | 0.488 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.487 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.487 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.486 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.483 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.482 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.481 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.478 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.478 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.478 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.478 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.476 | |
| 4nv1 | TYD | Formyl transferase | / | 0.476 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.474 | |
| 4to6 | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.474 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.472 | |
| 3b8x | G4M | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.472 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.472 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.472 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.472 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.472 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.472 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.471 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.471 | |
| 3r8h | ZOM | Aldo-keto reductase family 1 member C3 | / | 0.470 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 4kxj | P34 | Nucleoprotein | / | 0.469 | |
| 4to2 | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.469 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.468 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.468 | |
| 4dbu | BT9 | Aldo-keto reductase family 1 member C3 | / | 0.467 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.466 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.465 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.465 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.465 | |
| 3ele | PLP | Aminotransferase | / | 0.464 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.464 | |
| 1rxj | BNI | Streptavidin | / | 0.463 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.463 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.463 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.463 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.462 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.462 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.461 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.461 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.461 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 3tvq | DQH | Multifunctional cyclase-dehydratase-3-O-methyl transferase TcmN | 2.1.1 | 0.461 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.460 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1qs2 | NAD | Vip2Ac | / | 0.459 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.459 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.459 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.459 | |
| 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 | 0.458 | |
| 4jt9 | 1NS | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.458 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.457 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.457 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.456 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.456 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.456 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.456 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.455 | |
| 3ojg | HL4 | Phosphotriesterase | / | 0.455 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.455 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.455 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.455 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.455 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.454 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.454 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.454 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.454 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.453 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4e2y | JHZ | Methyltransferase | / | 0.453 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3e6e | DCS | Alanine racemase | / | 0.452 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.452 | |
| 4iks | TFD | Methionine aminopeptidase 1 | / | 0.452 | |
| 4lcn | GNG | Cytidine and deoxycytidylate deaminase zinc-binding region | / | 0.452 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.451 | |
| 1kyy | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.451 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 3w5u | FAD | Ferredoxin | / | 0.451 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 4drm | 0MC | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.451 | |
| 4mr7 | 2BV | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.450 | |
| 4rxp | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.450 | |
| 1a9c | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.449 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.449 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.449 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 3opm | LUI | Dipeptidyl peptidase 4 | / | 0.449 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.449 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.449 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.449 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.448 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.448 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 5jqh | CAU | Beta-2 adrenergic receptor | / | 0.448 | |
| 1w35 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.447 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.447 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.447 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1wkg | POI | [LysW]-aminoadipate semialdehyde transaminase | / | 0.446 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.446 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.446 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.446 | |
| 3ug8 | IMN | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.445 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.445 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.445 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.445 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.445 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.445 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1az2 | NAP | Aldose reductase | 1.1.1.21 | 0.444 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.443 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.443 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.443 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.443 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.443 | |
| 4fa3 | 0SL | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.443 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.443 | |
| 1e62 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.442 | |
| 1pj6 | FOL | Dimethylglycine oxidase | 1.5.3.10 | 0.442 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3ccc | 7AC | Dipeptidyl peptidase 4 | / | 0.442 | |
| 4c13 | UML | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase | / | 0.442 | |
| 4kn2 | LYA | Folate receptor beta | / | 0.442 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.442 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.441 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 1j0b | 5PA | Putative 1-aminocyclopropane-1-carboxylate deaminase | 3.5.99.7 | 0.440 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.440 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.440 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.440 | |
| 4b66 | FAD | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.440 |