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 |
|---|---|---|---|
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 1.000 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.693 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.645 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.644 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.622 | |
| 1lso | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.586 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.567 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.505 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.491 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.489 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.485 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.480 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.478 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.478 | |
| 1eio | GCH | Gastrotropin | / | 0.475 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.471 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.469 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.468 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.467 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.466 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.466 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.466 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.466 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.465 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.465 | |
| 2ejz | SAH | Diphthine synthase | / | 0.465 | |
| 3b9l | AZZ | Serum albumin | / | 0.464 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 4qec | NAP | ElxO | / | 0.463 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.461 | |
| 3p6p | A6B | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 4aa4 | QC0 | Mitogen-activated protein kinase 14 | / | 0.461 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.461 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.461 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.460 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.460 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.460 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.460 | |
| 3gob | HXX | DdmC | / | 0.460 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.460 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.460 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.459 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.459 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.458 | |
| 1ahi | CHO | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.457 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.457 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.457 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.456 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.454 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.454 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.454 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.454 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.454 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.453 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.453 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.453 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.452 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.452 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.452 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.452 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.452 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.451 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.450 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.450 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.450 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.450 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.450 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.449 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.449 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.449 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.449 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.449 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.448 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.448 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.448 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.447 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.447 | |
| 4px9 | ADP | ATP-dependent RNA helicase DDX3X | 3.6.4.13 | 0.447 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.447 | |
| 1osv | CHC | Bile acid receptor | / | 0.446 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.446 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.446 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.445 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.445 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.445 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.445 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.444 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.444 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.444 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.444 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.443 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.443 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.442 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.442 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.442 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.442 | |
| 4yt5 | H4M | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | / | 0.442 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.441 | |
| 1ez4 | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.441 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.441 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.441 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.441 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.441 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4ck2 | NVU | Integrase | / | 0.441 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.441 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.440 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.440 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.440 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.440 |