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 |
|---|---|---|---|
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 1.000 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.566 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.529 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.498 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.497 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.496 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.494 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.489 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.488 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.484 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.483 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.482 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.482 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.481 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.478 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.478 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.475 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.474 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.474 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.471 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.471 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.471 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.469 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.469 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.469 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.468 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.468 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.467 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.467 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.467 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.466 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.466 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.464 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.464 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.463 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.463 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.461 | |
| 1c7o | PPG | Hemolysin | / | 0.461 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.461 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.461 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.461 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.460 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.459 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.459 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.459 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.459 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.459 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.459 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.459 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.459 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.459 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.459 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.458 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.457 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.456 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.456 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.456 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.455 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.455 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 1vf3 | GDN | Glutathione S-transferase 3 | 2.5.1.18 | 0.454 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.454 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.454 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.453 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.453 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.453 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 4lut | DCS | Alanine racemase | / | 0.453 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.452 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.452 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.451 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.451 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.451 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.450 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.450 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.450 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.450 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.450 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.449 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.449 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 3e30 | ED4 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.449 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.449 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.449 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.449 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.449 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.449 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.448 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.448 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.448 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.447 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.447 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 1q23 | FUA | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.446 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.446 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.446 | |
| 5bv3 | M7G | m7GpppX diphosphatase | 3.6.1.59 | 0.446 | |
| 1o86 | LPR | Angiotensin-converting enzyme | 3.2.1 | 0.445 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.445 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.445 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.445 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.445 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.445 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.444 | |
| 1s63 | 778 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.444 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.444 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.444 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.444 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.444 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.444 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1uxy | EPU | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.443 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.443 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.443 | |
| 3ieu | GDP | GTPase Era | / | 0.443 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.443 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.443 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.442 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.442 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.442 | |
| 2oz5 | 7XY | Uncharacterized protein | / | 0.442 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.442 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.441 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.441 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.441 | |
| 3rvh | HQ2 | Lysine-specific demethylase 4A | 1.14.11 | 0.441 | |
| 4de2 | DN3 | Beta-lactamase | / | 0.441 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.441 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.440 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.440 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.440 | |
| 3n0b | FAD | Flavin-dependent thymidylate synthase | 2.1.1.148 | 0.440 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.440 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.440 |