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 |
|---|---|---|---|
| 3vi4 | ARG_GLY_ASP_ASN | Integrin beta-1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3vi4 | ARG_GLY_ASP_ASN | Integrin beta-1 | / | 1.000 | |
| 3vi4 | ARG_GLY_ASP_ASN | Integrin alpha-5 | / | 1.000 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.491 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.483 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.480 | |
| 3ngq | 1PS | CCR4-NOT transcription complex subunit 6-like | 3.1.13.4 | 0.478 | |
| 4ba5 | PXG | Probable aminotransferase | / | 0.478 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.475 | |
| 2ed4 | NAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.475 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.473 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.471 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.470 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4bb2 | STR | Corticosteroid-binding globulin | / | 0.470 | |
| 2e07 | SAH | Diphthine synthase | / | 0.469 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.469 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.468 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.468 | |
| 3eks | CY9 | Actin-5C | / | 0.468 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.466 | |
| 2e08 | SAH | Diphthine synthase | / | 0.466 | |
| 1wng | SAH | Diphthine synthase | / | 0.465 | |
| 3pft | FMN | Flavin reductase | / | 0.465 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.465 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.465 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.464 | |
| 3i6i | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.463 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.463 | |
| 3m2r | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.463 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.463 | |
| 4wx2 | F6F | Tryptophan synthase alpha chain | / | 0.463 | |
| 4wx2 | F6F | Tryptophan synthase beta chain | 4.2.1.20 | 0.463 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 2ejz | SAH | Diphthine synthase | / | 0.462 | |
| 2p9d | SAH | Diphthine synthase | / | 0.462 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.461 | |
| 2egb | SAH | Diphthine synthase | / | 0.461 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.461 | |
| 1vce | SAH | Diphthine synthase | / | 0.460 | |
| 2el0 | SAH | Diphthine synthase | / | 0.460 | |
| 4blr | UTP | NTPase P4 | / | 0.460 | |
| 4bri | UNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.460 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.459 | |
| 2owg | SAH | Diphthine synthase | / | 0.459 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.459 | |
| 3c6p | 2S3 | Protein TRANSPORT INHIBITOR RESPONSE 1 | / | 0.459 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.459 | |
| 2pca | SAH | Diphthine synthase | / | 0.458 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.457 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.457 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3i7v | B4P | AP4A hydrolase | / | 0.457 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.457 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.457 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.456 | |
| 3eku | CY9 | Actin-5C | / | 0.456 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.456 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.456 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.455 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.455 | |
| 1n75 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.454 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 3lm1 | LEC | Agglutinin alpha chain | / | 0.454 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.454 | |
| 1n8w | COA | Malate synthase G | / | 0.453 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.453 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.453 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.453 | |
| 2huq | SAH | Diphthine synthase | / | 0.453 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.453 | |
| 3p8h | P8H | Lethal(3)malignant brain tumor-like protein 1 | / | 0.453 | |
| 4lnb | ED5 | CaaX farnesyltransferase beta subunit Ram1 | / | 0.453 | |
| 4lut | DCS | Alanine racemase | / | 0.453 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.453 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.453 | |
| 2e7r | SAH | Diphthine synthase | / | 0.452 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.452 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.452 | |
| 2egs | SAH | Diphthine synthase | / | 0.451 | |
| 3b9x | NOS | Pyrimidine-specific ribonucleoside hydrolase RihB | 3.2.2.8 | 0.451 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.451 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 2emr | SAH | Diphthine synthase | / | 0.450 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.450 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.450 | |
| 1t57 | FMN | Conserved protein | / | 0.449 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.449 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.449 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.449 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.449 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.449 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4tlx | FDA | KtzI | / | 0.449 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.449 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.448 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.448 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.448 | |
| 2e4n | SAH | Diphthine synthase | / | 0.448 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.448 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.448 | |
| 4z87 | GDP | Inosine-5'-monophosphate dehydrogenase | / | 0.448 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.447 | |
| 2owu | SAH | Diphthine synthase | / | 0.447 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.447 | |
| 2ejj | SAH | Diphthine synthase | / | 0.446 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.446 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3c6o | 2S2 | Protein TRANSPORT INHIBITOR RESPONSE 1 | / | 0.446 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.446 | |
| 4yfy | 0FX | VioF | / | 0.446 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.445 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2bb3 | SAH | Cobalamin biosynthesis precorrin-6Y methylase (CbiE) | / | 0.445 | |
| 2dxx | SAH | Diphthine synthase | / | 0.445 | |
| 2eni | SAH | Diphthine synthase | / | 0.445 | |
| 2owb | 626 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.445 | |
| 3aos | JH2 | Hemolymph juvenile hormone binding protein | / | 0.445 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.445 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.445 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.445 | |
| 4nv1 | TYD | Formyl transferase | / | 0.445 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.444 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.444 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.444 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4w5k | PLP | Aspartate aminotransferase, mitochondrial | / | 0.444 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 5cho | FAD | Flavin reductase | / | 0.444 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.443 | |
| 1i7c | MGB | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.443 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.443 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3g2h | KOT | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.443 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.443 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.443 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.443 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.443 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.442 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1vf3 | GDN | Glutathione S-transferase 3 | 2.5.1.18 | 0.442 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2huv | SAH | Diphthine synthase | / | 0.442 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.442 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.442 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.442 | |
| 3gya | COA | GCN5-related N-acetyltransferase | / | 0.442 | |
| 4f9g | C2E | Stimulator of interferon genes protein | / | 0.442 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.442 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.441 | |
| 2pci | SAH | Diphthine synthase | / | 0.441 | |
| 2pck | SAH | Diphthine synthase | / | 0.441 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.441 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.441 | |
| 2xda | JPS | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.441 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.441 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4yfy | 1YJ | VioF | / | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.440 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.440 | |
| 1zha | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.440 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.440 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.440 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.440 | |
| 2p6i | SAH | Diphthine synthase | / | 0.440 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.440 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.440 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.440 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.440 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.440 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.440 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 |