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 |
|---|---|---|---|
| 5dbv | COA | Aldehyde Dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5dbv | COA | Aldehyde Dehydrogenase | / | 1.000 | |
| 4c3s | NAD | Aldehyde Dehydrogenase | / | 0.577 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.497 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.485 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.483 | |
| 4fg8 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.480 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.471 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.470 | |
| 3r5z | F42 | Uncharacterized protein | / | 0.469 | |
| 4die | C5P | Cytidylate kinase | / | 0.468 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.468 | |
| 2y3r | TRK | TamL | / | 0.466 | |
| 4l04 | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.466 | |
| 4l06 | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.466 | |
| 2y4g | TIR | TamL | / | 0.464 | |
| 3cgd | COA | Coenzyme A disulfide reductase | / | 0.464 | |
| 4k33 | ACP | Fibroblast growth factor receptor 3 | 2.7.10.1 | 0.464 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.463 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.463 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.463 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.462 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.462 | |
| 2ylw | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.461 | |
| 2ym1 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.461 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.461 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.459 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.459 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.459 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.458 | |
| 3c4x | ATP | Rhodopsin kinase | / | 0.458 | |
| 4d86 | ADP | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.458 | |
| 4h4z | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.458 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.458 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.457 | |
| 3cgb | COA | Coenzyme A disulfide reductase | / | 0.456 | |
| 4fg7 | ATP | Calcium/calmodulin-dependent protein kinase type 1 | 2.7.11.17 | 0.456 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.455 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.455 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.455 | |
| 2vht | ATP | NTPase P4 | / | 0.454 | |
| 3wow | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.454 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.454 | |
| 4ovi | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.454 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.453 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.453 | |
| 2c6d | ANP | Aurora kinase A | 2.7.11.1 | 0.453 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 2qrd | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.453 | |
| 4d04 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.453 | |
| 4fsr | HKC | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.453 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.453 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.452 | |
| 2vqb | NAP | Putative flavin-containing monooxygenase | / | 0.452 | |
| 4jia | 1K3 | Tyrosine-protein kinase JAK2 | / | 0.452 | |
| 1bdq | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 2nom | DUT | Poly(A) polymerase, putative | / | 0.451 | |
| 4bl1 | ANP | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.451 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.451 | |
| 4zse | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.451 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.450 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.450 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.450 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.450 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 4otw | DB8 | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.450 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.450 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.449 | |
| 1ny3 | ADP | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.449 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.449 | |
| 3uqd | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.449 | |
| 4g3q | UD1 | Bifunctional protein GlmU | / | 0.449 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.448 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.448 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.448 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.448 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.448 | |
| 4cpd | NAD | Alcohol dehydrogenase | / | 0.448 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.448 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.448 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.447 | |
| 2q64 | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 2xlr | NAP | Putative flavin-containing monooxygenase | / | 0.447 | |
| 2y3s | TIR | TamL | / | 0.447 | |
| 4kb9 | G79 | Protease | / | 0.447 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.446 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.446 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.446 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.446 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.446 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.446 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.446 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.446 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.446 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.445 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.445 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.445 | |
| 4lx9 | ACO | N-alpha-acetyltransferase | 2.3.1 | 0.445 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.445 | |
| 1me8 | RVP | Inosine-5'-monophosphate dehydrogenase | / | 0.444 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.444 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.444 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.444 | |
| 4kqr | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.444 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.444 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.444 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.443 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.443 | |
| 2qoc | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.443 | |
| 3eky | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 5ahs | COA | Acyl-CoA dehydrogenase | / | 0.443 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.442 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.442 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.442 | |
| 2hen | ADP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.442 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.442 | |
| 3ort | AGS | Serine/threonine protein kinase | / | 0.442 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.442 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.442 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.442 | |
| 1ebw | BEI | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.441 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.441 | |
| 2xch | CKG | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.441 | |
| 2bdf | 24A | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.440 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 2qhy | MZ1 | Gag-Pol polyprotein | / | 0.440 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.440 | |
| 3ekx | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.440 | |
| 3t8o | ATP | Rhodopsin kinase | / | 0.440 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.440 | |
| 4g3p | UD1 | Bifunctional protein GlmU | / | 0.440 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.440 | |
| 4xx9 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 |