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 |
|---|---|---|---|
| 5ch7 | MGD | DMSO reductase family type II enzyme, molybdopterin subunit |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5ch7 | MGD | DMSO reductase family type II enzyme, molybdopterin subunit | / | 1.000 | |
| 4ydd | MGD | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.611 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.492 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.492 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.492 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.485 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.484 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.482 | |
| 3wle | NAD | (R)-specific carbonyl reductase | / | 0.482 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.479 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.478 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.477 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.475 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.473 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.472 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.471 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.470 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.470 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.470 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.469 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.468 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.467 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.466 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.466 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.465 | |
| 1wng | SAH | Diphthine synthase | / | 0.465 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.465 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.465 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.465 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.464 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.463 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.463 | |
| 2zdy | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.463 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.463 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.463 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.463 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.463 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.462 | |
| 3jzi | JZL | Biotin carboxylase | 6.3.4.14 | 0.462 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.462 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.461 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.460 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.460 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.460 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.460 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.460 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.460 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.459 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.459 | |
| 3uce | NDP | Dehydrogenase | / | 0.459 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.459 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.458 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.458 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.458 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.458 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.458 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.458 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.457 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.457 | |
| 2e8h | SAH | Diphthine synthase | / | 0.457 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.457 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.457 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.457 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.456 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.456 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.456 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.456 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.455 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.455 | |
| 2p6l | SAH | Diphthine synthase | / | 0.455 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.454 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.454 | |
| 2dph | NAD | Formaldehyde dismutase | / | 0.454 | |
| 2ejk | SAH | Diphthine synthase | / | 0.454 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.453 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.453 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.453 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.453 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.453 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4mqt | 2CU | Muscarinic acetylcholine receptor M2 | / | 0.453 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.452 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.452 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.452 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.452 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.452 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2p5c | SAH | Diphthine synthase | / | 0.451 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.451 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.451 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.451 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.451 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.450 | |
| 1t3z | CAO | Formyl-CoA:oxalate CoA-transferase | / | 0.450 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.450 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.450 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.450 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.450 | |
| 4ovi | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.450 | |
| 5dmh | ADP | 3-oxo-tetronate kinase | / | 0.450 | |
| 1muu | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.449 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.449 | |
| 2egs | SAH | Diphthine synthase | / | 0.449 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.449 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.449 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.449 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.449 | |
| 5dst | SAH | Protein arginine N-methyltransferase 8 | 2.1.1 | 0.449 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.448 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.448 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.448 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.448 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.448 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.447 | |
| 1mei | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.447 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.447 | |
| 2egb | SAH | Diphthine synthase | / | 0.447 | |
| 2emr | SAH | Diphthine synthase | / | 0.447 | |
| 2emu | SAH | Diphthine synthase | / | 0.447 | |
| 2ylw | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.447 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.447 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.447 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.447 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.447 | |
| 3jyo | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.447 | |
| 3v3m | 0EN | Replicase polyprotein 1a | 3.4.19.12 | 0.447 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.447 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.447 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.446 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.446 | |
| 2e7r | SAH | Diphthine synthase | / | 0.446 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.446 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.446 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.446 | |
| 4l98 | LRG | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.446 | |
| 5bqf | NAP | Probable hydroxyacid dehydrogenase protein | / | 0.446 | |
| 1njj | ORX | Ornithine decarboxylase | / | 0.445 | |
| 1z5c | ADP | Type 2 DNA topoisomerase 6 subunit B | / | 0.445 | |
| 2ejz | SAH | Diphthine synthase | / | 0.445 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.445 | |
| 3kp4 | MII | Transcriptional regulator TcaR | / | 0.445 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.445 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.445 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.445 | |
| 1dq9 | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.444 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.444 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.444 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.444 | |
| 1xef | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.444 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.444 | |
| 2ol4 | JPN | Enoyl-ACP reductase | / | 0.444 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.444 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.444 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.444 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.444 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.443 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.443 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.443 | |
| 1tys | DHF | Thymidylate synthase | / | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.443 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.443 | |
| 2p6i | SAH | Diphthine synthase | / | 0.443 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.443 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.443 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.443 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.443 | |
| 1ptj | NAP | NAD(P) transhydrogenase subunit beta | 1.6.1.2 | 0.442 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.442 | |
| 1yzq | GNP | Ras-related protein Rab-6A | / | 0.442 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.442 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 | 0.442 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.442 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 3kr6 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.442 | |
| 3r96 | ACO | MccE protein | / | 0.442 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.442 | |
| 4d9f | DCS | D-cysteine desulfhydrase | / | 0.442 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.442 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.442 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.441 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.441 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.441 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.441 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.441 | |
| 2eld | SAH | Diphthine synthase | / | 0.441 | |
| 2gtb | AZP | Orf1ab polyprotein | / | 0.441 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.441 | |
| 3amf | FMN | FMN-binding protein | / | 0.441 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.441 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 3pdn | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.441 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.441 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.441 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.441 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 1a2n | TET | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.440 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.440 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.440 | |
| 1w1w | AGS | Structural maintenance of chromosomes protein 1 | / | 0.440 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2e4n | SAH | Diphthine synthase | / | 0.440 | |
| 2eni | SAH | Diphthine synthase | / | 0.440 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.440 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.440 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.440 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.440 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4h4z | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.440 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.440 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.440 | |
| 5hq8 | SAH | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.440 |