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 |
|---|---|---|---|
| 1gl3 | NDP | Aspartate-semialdehyde dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1gl3 | NDP | Aspartate-semialdehyde dehydrogenase | / | 1.000 | |
| 1mb4 | NDP | Aspartate-semialdehyde dehydrogenase 1 | / | 0.529 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.510 | |
| 3pzr | NAP | Aspartate-semialdehyde dehydrogenase 1 | / | 0.488 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.481 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.481 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.480 | |
| 3u9e | COA | Lmo1369 protein | / | 0.479 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.476 | |
| 3gob | HXX | DdmC | / | 0.476 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.475 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.475 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.475 | |
| 3pgq | GY3 | Acetyl-CoA carboxylase | / | 0.474 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.473 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.473 | |
| 2p20 | PRX | Acetyl-coenzyme A synthetase | / | 0.472 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.472 | |
| 1ha3 | MAU | Elongation factor Tu-A | / | 0.470 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.468 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.467 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.467 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.466 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.466 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.466 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.464 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.463 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.463 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.463 | |
| 3w2l | VRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.463 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.462 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.462 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.462 | |
| 3ojx | FAD | NADPH--cytochrome P450 reductase | / | 0.462 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.461 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.461 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 2e0a | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.460 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.460 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.459 | |
| 2e9u | A25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.459 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.459 | |
| 3a3b | RBF | Lumazine protein | / | 0.459 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.459 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.459 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.458 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.457 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.456 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.456 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.455 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 4irn | FAD | AnaB | / | 0.455 | |
| 1f20 | NAP | Nitric oxide synthase, brain | 1.14.13.39 | 0.454 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.454 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.454 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.454 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.453 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.453 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.452 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.452 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.452 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.452 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.451 | |
| 2jcx | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.451 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 0.451 | |
| 1dj2 | GDP | Adenylosuccinate synthetase, chloroplastic | / | 0.450 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.450 | |
| 1j1b | ANP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.450 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.450 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.450 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.450 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.450 | |
| 3w23 | 3RO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.450 | |
| 4e2d | FMN | Dehydrogenase | / | 0.450 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 5cts | CMC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.450 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.449 | |
| 2w02 | ATP | AcsD | / | 0.449 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.449 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.449 | |
| 2e9d | B76 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.448 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.448 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.448 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.448 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.447 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.447 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.447 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.447 | |
| 3ii4 | 3II | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.447 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.447 | |
| 4jic | FMN | GTN Reductase | / | 0.447 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.447 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.447 | |
| 5bmv | VLB | Tubulin alpha-1B chain | / | 0.447 | |
| 5bmv | VLB | Tubulin beta chain | / | 0.447 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.446 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 2ohv | NHL | Glutamate racemase | / | 0.446 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.446 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 3u8l | 09Q | Acetylcholine-binding protein | / | 0.446 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.446 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.446 | |
| 1u54 | ACP | Activated CDC42 kinase 1 | / | 0.445 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.445 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2g2z | COZ | Malonyl CoA-acyl carrier protein transacylase | 2.3.1.39 | 0.445 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.445 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.445 | |
| 2zdy | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.445 | |
| 3a3g | DLZ | Lumazine protein | / | 0.445 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.445 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 5cyo | GDP | Septin-9 | / | 0.445 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.444 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.444 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.444 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 4dja | FAD | (6-4) photolyase | / | 0.444 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.444 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.444 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.444 | |
| 1sxj | AGS | Replication factor C subunit 1 | / | 0.443 | |
| 2ii6 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.443 | |
| 2uzt | SS3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2wb2 | FAD | RE11660p | / | 0.443 | |
| 3fpj | SAM | Uncharacterized protein | / | 0.443 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.443 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4im0 | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.443 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.443 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.442 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 1pvg | ANP | DNA topoisomerase 2 | 5.99.1.3 | 0.442 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.442 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2yye | APC | Selenide, water dikinase | 2.7.9.3 | 0.442 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.442 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.442 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.442 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.441 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.441 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3h4l | ANP | DNA mismatch repair protein PMS1 | / | 0.441 | |
| 4bie | IE6 | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.441 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.440 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.440 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.440 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.440 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.440 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.440 | |
| 3v3m | 0EN | Replicase polyprotein 1a | 3.4.19.12 | 0.440 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.440 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.440 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.440 | |
| 4xbo | SAH | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | 2.1.1.200 | 0.440 | |
| 4xj4 | 3AT | Cyclic GMP-AMP synthase | / | 0.440 | |
| 4zse | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 5a9s | NAP | Putative dehydrogenase | / | 0.440 | |
| 5dac | AGS | Uncharacterized protein | / | 0.440 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.440 | |
| 5il2 | SAH | N6-adenosine-methyltransferase 70 kDa subunit | / | 0.440 |