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 |
|---|---|---|---|
| 3pqf | NAD | L-lactate dehydrogenase | 1.1.1.27 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3pqf | NAD | L-lactate dehydrogenase | 1.1.1.27 | 1.000 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.576 | |
| 4rls | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.570 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.548 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.540 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.537 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.526 | |
| 1ez4 | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.522 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.520 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.510 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.505 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.498 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.497 | |
| 2ldb | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.495 | |
| 1wzi | NDP | Malate dehydrogenase | / | 0.494 | |
| 1bdm | NAX | Malate dehydrogenase | / | 0.490 | |
| 1b8u | NAD | Malate dehydrogenase | / | 0.487 | |
| 4ajn | 88V | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.487 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.487 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.486 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.484 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.483 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.483 | |
| 1llq | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.482 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.482 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.481 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.476 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.475 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.474 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.473 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.473 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.472 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.472 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.471 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.471 | |
| 4qec | NAP | ElxO | / | 0.471 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.469 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 1wze | NAD | Malate dehydrogenase | / | 0.468 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.468 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.467 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.467 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.464 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.464 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.463 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.463 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.463 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.462 | |
| 3b9l | AZZ | Serum albumin | / | 0.462 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.462 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.462 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.461 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.461 | |
| 4txz | G2P | Cyclic GMP-AMP synthase | / | 0.461 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 3uce | NDP | Dehydrogenase | / | 0.460 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.460 | |
| 1qr6 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.459 | |
| 3mk6 | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.459 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.459 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.458 | |
| 4ajj | 88R | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.458 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.458 | |
| 4i9h | 1E4 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.458 | |
| 1o6z | NAD | Malate dehydrogenase | / | 0.457 | |
| 2ejz | SAH | Diphthine synthase | / | 0.457 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.457 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.456 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.456 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.456 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.456 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.456 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.455 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.455 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.455 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.455 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.455 | |
| 1bmd | NAD | Malate dehydrogenase | / | 0.454 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.453 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.453 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.452 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.452 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.452 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.452 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.452 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.451 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.451 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.451 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.451 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.450 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.450 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.450 | |
| 3otf | CMP | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.450 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.450 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.450 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.449 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.449 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.449 | |
| 3ms4 | 21N | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.449 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.449 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.449 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.449 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.448 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.448 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.448 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.448 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.448 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.447 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.447 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 4l4x | NDP | AmphI | / | 0.447 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.446 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.446 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.446 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.446 | |
| 4xb2 | NDP | 319aa long hypothetical homoserine dehydrogenase | / | 0.446 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.446 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.445 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.445 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.445 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.445 | |
| 3r96 | ACO | MccE protein | / | 0.445 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4uun | NAI | L-lactate dehydrogenase | / | 0.445 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.444 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.444 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.444 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.444 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.444 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.444 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.444 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.444 | |
| 1gjv | AGS | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | 2.7.11.4 | 0.443 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.443 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.443 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.443 | |
| 2zsi | GA4 | Gibberellin receptor GID1A | 3 | 0.443 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 3rk1 | ATP | N-type ATP pyrophosphatase superfamily | / | 0.443 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.443 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.443 | |
| 4h30 | 0ZD | Macrophage metalloelastase | 3.4.24.65 | 0.443 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.443 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.443 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.442 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.442 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 2zax | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.442 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.441 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.441 | |
| 3bmo | NAP | Pteridine reductase | / | 0.441 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.441 | |
| 4e2d | FMN | Dehydrogenase | / | 0.441 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.441 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.440 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.440 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2hld | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.440 | |
| 2hld | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.440 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.440 | |
| 2y3s | TIR | TamL | / | 0.440 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 |