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 |
|---|---|---|---|
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 1.000 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.632 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.630 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.624 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.616 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.608 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.584 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.570 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.501 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.493 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.493 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.488 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.487 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.487 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.485 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.485 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.482 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.478 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.476 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.475 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.475 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.475 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.474 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.473 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.470 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.468 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.467 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.467 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.467 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.467 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.465 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.465 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.465 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.465 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.462 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.462 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2bxo | OPB | Serum albumin | / | 0.461 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.460 | |
| 4iae | 1DX | Alr2278 protein | / | 0.460 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.459 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4iah | 1DX | Alr2278 protein | / | 0.458 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.457 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3cas | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.454 | |
| 3eku | CY9 | Actin-5C | / | 0.454 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.454 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.453 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.453 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.452 | |
| 3fap | ARD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.452 | |
| 3fap | ARD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.452 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.452 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.451 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.450 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.450 | |
| 1q23 | FUA | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.450 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.450 | |
| 2vqq | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.450 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.450 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2hps | CTZ | Ca2+-triggered coelenterazine-binding protein 1 | / | 0.449 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 1lke | DOG | Bilin-binding protein | / | 0.448 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.448 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.448 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 1by5 | GLY_GLY_GLY_AHO_AHO_AHO_FE | Ferrichrome-iron receptor | / | 0.447 | |
| 1r2j | FAD | FkbI | / | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.447 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.447 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.447 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.447 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.447 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.447 | |
| 1c7o | PPG | Hemolysin | / | 0.446 | |
| 1eio | GCH | Gastrotropin | / | 0.446 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2aot | 2PM | Histamine N-methyltransferase | 2.1.1.8 | 0.446 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.446 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.446 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.446 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1p91 | SAM | 23S rRNA (guanine(745)-N(1))-methyltransferase | / | 0.445 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 3uon | QNB | Muscarinic acetylcholine receptor M2 | / | 0.445 | |
| 1dtp | APU | Diphtheria toxin | / | 0.444 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.444 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.444 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.443 | |
| 2ejz | SAH | Diphthine synthase | / | 0.443 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.443 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.443 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.443 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.443 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.443 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.443 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.442 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.442 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.442 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3v2u | ATP | Protein GAL3 | / | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.440 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4lut | DCS | Alanine racemase | / | 0.440 | |
| 4xo7 | ASD | Aldo-keto reductase family 1 member C2 | / | 0.440 |