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 |
|---|---|---|---|
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 1.000 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.636 | |
| 3kme | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.599 | |
| 2i47 | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.596 | |
| 2i47 | KGY | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.594 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.563 | |
| 3e8r | 615 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.562 | |
| 2a8h | 4NH | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.539 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.539 | |
| 3le9 | 727 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.536 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.530 | |
| 3l0v | 724 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.513 | |
| 3l0t | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.501 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.493 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.491 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.490 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.480 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.477 | |
| 2yj5 | ATP | Copper-transporting ATPase | / | 0.476 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.475 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.473 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.472 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.471 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.471 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.470 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.470 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.468 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.468 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.468 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.467 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.467 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.465 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.465 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.463 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.463 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.463 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.463 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.461 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.461 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.460 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.460 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.460 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.460 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.459 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4fkz | UD1 | UDP-N-acetylglucosamine 2-epimerase | 5.1.3.14 | 0.459 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.459 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.459 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.458 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.458 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.458 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.457 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.457 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.457 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.457 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.457 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.456 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.456 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.456 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.456 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.456 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.455 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.455 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.455 | |
| 4jlc | SU6 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.455 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.454 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 3nbv | ANP | Ketohexokinase | / | 0.454 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.454 | |
| 4f65 | 0S9 | Fibroblast growth factor receptor 1 | / | 0.454 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.453 | |
| 2wer | RDC | ATP-dependent molecular chaperone HSP82 | / | 0.453 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.453 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.453 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.453 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.453 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.453 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 2gd6 | ACO | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.452 | |
| 2w14 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.452 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.452 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.452 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 3vcy | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.452 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.452 | |
| 4g6h | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.452 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.452 | |
| 4rrh | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.452 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.451 | |
| 3ama | SKE | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.451 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.451 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.451 | |
| 1n2h | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.450 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.450 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.450 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.449 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.449 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.449 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.449 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.449 | |
| 3kds | NHX | ATP-dependent zinc metalloprotease FtsH | / | 0.449 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.448 | |
| 4g73 | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.448 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.447 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.447 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.446 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.446 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.446 | |
| 2y8l | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.446 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.446 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.446 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.446 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.446 | |
| 6gsw | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.446 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.445 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.445 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.445 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.445 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.445 | |
| 2p5f | SAH | Diphthine synthase | / | 0.445 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2qdx | FAD | Ferredoxin--NADP+ reductase | / | 0.445 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.445 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3c11 | GDM | ATP-dependent molecular chaperone HSP82 | / | 0.445 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.445 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.445 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2pam | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.444 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.444 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.444 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.444 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.444 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.443 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 4e2b | FMN | Dehydrogenase | / | 0.443 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4rr8 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.443 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.443 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.442 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.442 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.442 | |
| 1jmh | UMP | Thymidylate synthase | / | 0.442 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.442 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.442 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.442 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.442 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.441 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.441 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.441 | |
| 1jkx | 138 | Phosphoribosylglycinamide formyltransferase | / | 0.441 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.441 | |
| 2o4c | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.441 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.441 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.441 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.441 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.441 | |
| 3ooi | SAM | Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific | 2.1.1.43 | 0.441 | |
| 4a0r | DTB | Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial | 6.3.3.3 | 0.441 | |
| 4a6c | QG9 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.441 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.441 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.440 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.440 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.440 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.440 | |
| 2fgj | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.440 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 2w13 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.440 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3a3b | RBF | Lumazine protein | / | 0.440 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4ctk | SAM | Genome polyprotein | / | 0.440 | |
| 5dp2 | NAP | CurF | / | 0.440 |