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 |
|---|---|---|---|
| 3fun | 798 | Leukotriene A-4 hydrolase | 3.3.2.6 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3fun | 798 | Leukotriene A-4 hydrolase | 3.3.2.6 | 1.000 | |
| 3ful | 52D | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.830 | |
| 3fui | 812 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.718 | |
| 3ftx | BES | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.622 | |
| 4rsy | B3N | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.609 | |
| 3fuh | BES | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.590 | |
| 3fuj | 00G | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.585 | |
| 3chs | 4BU | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.550 | |
| 3fu5 | 492 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.536 | |
| 2r59 | PH0 | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.535 | |
| 4gaa | BES | Leukotriene A(4) hydrolase | / | 0.520 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.500 | |
| 3ogw | IMN | Lactoperoxidase | 1.11.1.7 | 0.498 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.484 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.482 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.480 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.478 | |
| 1lc3 | NAD | Biliverdin reductase A | 1.3.1.24 | 0.476 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.476 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.475 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.474 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.474 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.472 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 4z87 | GDP | Inosine-5'-monophosphate dehydrogenase | / | 0.471 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 3ndj | JHZ | Methyltransferase | / | 0.470 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.469 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.469 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.468 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.468 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.467 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.466 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.466 | |
| 4pne | SAH | Methyltransferase-like protein | / | 0.466 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.464 | |
| 4jbs | P52 | Endoplasmic reticulum aminopeptidase 2 | 3.4.11 | 0.464 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.463 | |
| 2b82 | ADN | Class B acid phosphatase | 3.1.3.2 | 0.463 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.463 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.462 | |
| 2ejz | SAH | Diphthine synthase | / | 0.461 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.461 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.461 | |
| 1txz | APR | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.460 | |
| 2h63 | NAP | Biliverdin reductase A | 1.3.1.24 | 0.460 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.460 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 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 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.459 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.458 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.458 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.458 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 3lq4 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.457 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.456 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.456 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.456 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4gv2 | 5ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.456 | |
| 4rv9 | SAH | D-mycarose 3-C-methyltransferase | / | 0.456 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.456 | |
| 1m9n | AMZ | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.455 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.455 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.455 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.455 | |
| 2wb2 | FAD | RE11660p | / | 0.455 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.455 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.454 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.454 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.454 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.453 | |
| 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 | 0.453 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.453 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.452 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.452 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.452 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3e4a | QIX | Insulin-degrading enzyme | 3.4.24.56 | 0.452 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.452 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.452 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.451 | |
| 3dr7 | GPD | GDP-perosamine synthase | / | 0.451 | |
| 4b66 | FAD | L-ornithine N(5)-monooxygenase | / | 0.451 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.451 | |
| 4e2z | JHZ | Methyltransferase | / | 0.451 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.449 | |
| 1tys | DHF | Thymidylate synthase | / | 0.449 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.449 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2v5u | FMN | Flavodoxin | / | 0.449 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.449 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.448 | |
| 3i7v | B4P | AP4A hydrolase | / | 0.448 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 3w2f | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4n3r | 2GU | Tankyrase-1 | 2.4.2.30 | 0.448 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.448 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.447 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.447 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.447 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.447 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.447 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.447 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3bt9 | DEQ | HTH-type transcriptional regulator QacR | / | 0.446 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.445 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.445 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.445 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.445 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 5dp2 | NAP | CurF | / | 0.445 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.445 | |
| 1aa6 | MGD | Formate dehydrogenase H | 1.1.99.33 | 0.444 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.444 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.444 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2npf | MOU | Elongation factor 2 | / | 0.444 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.444 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.444 | |
| 3wag | TYD | Glycosyltransferase | / | 0.444 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.444 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 5fuw | THM | Thymidine kinase, putative | / | 0.444 | |
| 1c7o | PPG | Hemolysin | / | 0.443 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.443 | |
| 3d4b | DZD | NAD-dependent protein deacetylase | / | 0.443 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4nt3 | ZAW | Lactoperoxidase | 1.11.1.7 | 0.443 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.443 | |
| 4y57 | F63 | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 1mzc | BNE | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.442 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.442 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.442 | |
| 3c8a | ARG_ARG_GLY_LEU_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.442 | |
| 3lcm | FAD | Putative oxidoreductase | / | 0.442 | |
| 3ssm | SAH | Mycinamicin VI 2''-O-methyltransferase | / | 0.442 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.442 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.442 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1wkh | PPE | [LysW]-aminoadipate semialdehyde transaminase | / | 0.441 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.441 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.441 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.441 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.441 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2vdy | HCY | Corticosteroid-binding globulin | / | 0.440 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3abx | RCB | Glucanase | / | 0.440 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.440 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4dym | IYZ | Activin receptor type-1 | 2.7.11.30 | 0.440 | |
| 4e32 | DWN | Methyltransferase | / | 0.440 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.440 |