sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 1.000 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.798 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.787 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.765 | |
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.751 | |
| 1lgt | BP3 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.576 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.541 | |
| 1kmy | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.493 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.491 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.483 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.478 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.478 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.474 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.473 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.473 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.472 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.472 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.472 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.471 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.471 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.471 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.470 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.470 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.469 | |
| 2dxi | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.469 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.469 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.468 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.468 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.468 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.466 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.464 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.463 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.463 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.463 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.462 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.462 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.462 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.462 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.462 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.461 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.461 | |
| 3gxf | IFM | Glucosylceramidase | 3.2.1.45 | 0.461 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.460 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.459 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.459 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.459 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.459 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.458 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.457 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.457 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.456 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.456 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.456 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.456 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.456 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.455 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.455 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.455 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.454 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.454 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.454 | |
| 5cho | FAD | Flavin reductase | / | 0.454 | |
| 1n95 | FTH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.453 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.453 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 4k36 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.453 | |
| 4rxp | DTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.453 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.452 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.452 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.452 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.452 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.452 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.452 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.452 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.452 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.451 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.451 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.450 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.450 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.450 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.450 | |
| 3hxd | BD7 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.450 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.450 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.450 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1el4 | CTZ | Obelin | / | 0.449 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.449 | |
| 1tys | TMP | Thymidylate synthase | / | 0.449 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.449 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.449 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.448 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.448 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 4g8c | C6L | Alpha/beta hydrolase fold protein | / | 0.448 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.447 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.447 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.447 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.447 | |
| 4n1g | CEI | Obelin | / | 0.447 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.447 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.447 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.446 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.446 | |
| 4std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.446 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 3g0c | RUF | Dipeptidyl peptidase 4 | / | 0.445 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.445 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.444 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.444 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.444 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.443 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.443 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.443 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.443 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.443 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4du6 | GTP | GTP cyclohydrolase 1 | / | 0.443 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 1vgr | COA | Formyl-CoA:oxalate CoA-transferase | / | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.442 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.442 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.442 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.442 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.442 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.442 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.441 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.441 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 3hbf | MYC | Flavonoid 3-O-glucosyltransferase | 2.4.1 | 0.441 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.441 | |
| 4e2d | FMN | Dehydrogenase | / | 0.441 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.440 | |
| 1lke | DOG | Bilin-binding protein | / | 0.440 | |
| 1qv0 | CZH | Obelin | / | 0.440 | |
| 2b3v | ACO | Diamine acetyltransferase 1 | / | 0.440 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.440 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.440 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.440 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.440 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.440 | |
| 3m67 | E36 | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.440 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.440 |