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 |
|---|---|---|---|
| 1emd | NAD | Malate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1emd | NAD | Malate dehydrogenase | / | 1.000 | |
| 1ib6 | NAD | Malate dehydrogenase | / | 0.632 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.562 | |
| 3h3j | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.547 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.543 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.543 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.540 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.535 | |
| 4ros | APR | Malate dehydrogenase | / | 0.535 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.530 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.525 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.525 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.524 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.519 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.519 | |
| 1ur5 | NAD | Malate dehydrogenase | / | 0.512 | |
| 3pqf | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.504 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.504 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.503 | |
| 3h3f | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.503 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.499 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.497 | |
| 1gv0 | NAD | Malate dehydrogenase | / | 0.496 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.495 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.495 | |
| 2dc1 | NAD | Probable L-aspartate dehydrogenase | / | 0.494 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.493 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.491 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.490 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.489 | |
| 4ajn | 88V | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.488 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.487 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.486 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.484 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.483 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.482 | |
| 4ajj | 88R | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.480 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.479 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.478 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.477 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.475 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.475 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.474 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.471 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.471 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.471 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.470 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.469 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.468 | |
| 3zzn | ADP | L-lactate dehydrogenase | / | 0.468 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.468 | |
| 3hx4 | ANP | Calmodulin-domain protein kinase 1 | / | 0.467 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.467 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.467 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.466 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.465 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.465 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.464 | |
| 2dsh | SAH | Diphthine synthase | / | 0.464 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.464 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.464 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.463 | |
| 3wsw | NAD | L-lactate dehydrogenase | / | 0.463 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.463 | |
| 2gz7 | D3F | Orf1a polyprotein | / | 0.462 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.461 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1w5t | ANP | ORC1-type DNA replication protein 2 | / | 0.460 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.460 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.460 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.459 | |
| 2dxv | SAH | Diphthine synthase | / | 0.459 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.458 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.458 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.457 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.456 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.456 | |
| 1q6t | 600 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.456 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.456 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.456 | |
| 2emr | SAH | Diphthine synthase | / | 0.455 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.455 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.455 | |
| 1d0m | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.454 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 4i9h | 1E4 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.454 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.453 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.453 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.453 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.453 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.452 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.452 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.452 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.452 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.452 | |
| 1mzs | 669 | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.451 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.451 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.451 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.451 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.451 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.451 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.451 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.451 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.450 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.450 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.450 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.450 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.449 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.449 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.449 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.449 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.449 | |
| 5a3b | APR | SIR2 family protein | / | 0.449 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 2e8q | SAH | Diphthine synthase | / | 0.448 | |
| 2ejz | SAH | Diphthine synthase | / | 0.448 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.448 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.448 | |
| 2pcm | SAH | Diphthine synthase | / | 0.448 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.448 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.447 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.447 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.447 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.447 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.447 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.447 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.447 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.447 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.447 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.447 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.446 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.446 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.446 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.446 | |
| 4fnc | HMU | G/T mismatch-specific thymine DNA glycosylase | 3.2.2.29 | 0.446 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.446 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.446 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 1lqu | NDP | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.445 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1r2j | FAD | FkbI | / | 0.445 | |
| 1u5a | BIK | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 2eka | SAH | Diphthine synthase | / | 0.445 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.445 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.445 | |
| 3mt8 | 17T | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.445 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.445 | |
| 4yqf | GDP | Septin-9 | / | 0.445 | |
| 1d7a | AIR | N5-carboxyaminoimidazole ribonucleotide mutase | / | 0.444 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.444 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.444 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.444 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.444 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.444 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.443 | |
| 1cde | DZF | Phosphoribosylglycinamide formyltransferase | / | 0.443 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.443 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.443 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.443 | |
| 2en5 | SAH | Diphthine synthase | / | 0.443 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.443 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.443 | |
| 3ieu | GDP | GTPase Era | / | 0.443 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.443 | |
| 3v2u | ATP | Protein GAL3 | / | 0.443 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.443 | |
| 4uun | NAI | L-lactate dehydrogenase | / | 0.443 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.442 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.442 | |
| 1kvk | ATP | Mevalonate kinase | 2.7.1.36 | 0.442 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1y7t | NDP | Malate dehydrogenase | / | 0.442 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.442 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.442 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.442 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.442 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.442 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.442 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.442 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.441 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.441 | |
| 1ja0 | NAP | NADPH--cytochrome P450 reductase | / | 0.441 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.441 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.441 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.441 | |
| 2eld | SAH | Diphthine synthase | / | 0.441 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.441 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.441 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.440 | |
| 2dsg | SAH | Diphthine synthase | / | 0.440 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.440 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.440 | |
| 2owk | SAH | Diphthine synthase | / | 0.440 | |
| 2p5f | SAH | Diphthine synthase | / | 0.440 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.440 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.440 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.440 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.440 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.440 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.440 | |
| 4ubv | COA | Steroid 3-ketoacyl-CoA thiolase | / | 0.440 | |
| 4uoc | NCN | CinA-like protein | / | 0.440 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.440 | |
| 5l3d | FAD | Lysine-specific histone demethylase 1A | 1 | 0.440 |