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 |
|---|---|---|---|
| 3nrc | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3nrc | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 1.000 | |
| 3uic | 09T | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.615 | |
| 3fnh | JPJ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.581 | |
| 5cp8 | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.574 | |
| 5coq | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.555 | |
| 3fne | 8PC | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.538 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.537 | |
| 4tzk | 641 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.536 | |
| 2o2y | TCL | Enoyl-ACP reductase | / | 0.533 | |
| 3lt2 | FT3 | Enoyl-ACP reductase | / | 0.533 | |
| 1nhg | TCL | Enoyl-ACP reductase | / | 0.531 | |
| 1zsn | TN2 | Enoyl-ACP reductase | / | 0.523 | |
| 1uh5 | TCL | Enoyl-ACP reductase | / | 0.519 | |
| 3lt1 | FT2 | Enoyl-ACP reductase | / | 0.516 | |
| 1zw1 | TN5 | Enoyl-ACP reductase | / | 0.515 | |
| 1zxl | JP1 | Enoyl-ACP reductase | / | 0.512 | |
| 2nsd | 4PI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.512 | |
| 3lsy | FT0 | Enoyl-ACP reductase | / | 0.512 | |
| 2op0 | 7PC | Enoyl-ACP reductase | / | 0.508 | |
| 3f4b | TCL | Enoyl-acyl carrier protein reductase | / | 0.508 | |
| 3lt0 | FT1 | Enoyl-ACP reductase | / | 0.508 | |
| 3am4 | FT1 | Enoyl-ACP reductase | / | 0.506 | |
| 3am5 | TCL | Enoyl-ACP reductase | / | 0.503 | |
| 1nnu | TCT | Enoyl-ACP reductase | / | 0.498 | |
| 3nj8 | NJ8 | Enoyl-acyl carrier reductase | / | 0.498 | |
| 2foi | JPA | Enoyl-acyl carrier reductase | / | 0.491 | |
| 3am3 | TCL | Enoyl-ACP reductase | / | 0.491 | |
| 2o2s | TCL | Enoyl-acyl carrier reductase | / | 0.490 | |
| 3fnf | JPM | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.488 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.483 | |
| 4u0k | 744 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.483 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.482 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.481 | |
| 4ige | CHJ | Enoyl-acyl carrier reductase | / | 0.481 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.477 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.477 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.477 | |
| 4trj | 665 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.476 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.472 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.471 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.471 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.469 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.468 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.467 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.467 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.467 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.466 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.466 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.466 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.466 | |
| 4ybn | FAD | Flavin-nucleotide-binding protein | / | 0.466 | |
| 1nhw | TCC | Enoyl-ACP reductase | / | 0.465 | |
| 2zb4 | 5OP | Prostaglandin reductase 2 | 1.3.1.48 | 0.464 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.464 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 2p2b | PRX | Acetyl-coenzyme A synthetase | / | 0.462 | |
| 4lvb | 20N | Nicotinamide phosphoribosyltransferase | 2.4.2.12 | 0.462 | |
| 3ipq | 965 | Oxysterols receptor LXR-alpha | / | 0.461 | |
| 3qgd | 26S | Genome polyprotein | 2.7.7.48 | 0.461 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.461 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.460 | |
| 1fml | RTL | Retinol dehydratase | / | 0.460 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.460 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.459 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.459 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.459 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.458 | |
| 1pg3 | PRX | Acetyl-coenzyme A synthetase | / | 0.457 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.457 | |
| 5c3a | URM | Histo-blood group ABO system transferase | / | 0.457 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.456 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.456 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.455 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.455 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.455 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.455 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.455 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 4mt9 | 2D6 | Tankyrase-1 | 2.4.2.30 | 0.455 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.455 | |
| 1axw | MTX | Thymidylate synthase | / | 0.454 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.454 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.454 | |
| 3iw1 | ASD | Steroid C26-monooxygenase | 1.14.13.141 | 0.454 | |
| 4msg | 2C6 | Tankyrase-1 | 2.4.2.30 | 0.454 | |
| 4rrw | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.454 | |
| 4rrz | LUR | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.454 | |
| 1jg0 | DDT | Thymidylate synthase | / | 0.453 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2p2j | PRX | Acetyl-coenzyme A synthetase | / | 0.453 | |
| 4b5d | SW4 | Achbp | / | 0.453 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.453 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.452 | |
| 3c16 | FOK | Adenylate cyclase type 2 | / | 0.452 | |
| 3c16 | FOK | Adenylate cyclase type 5 | / | 0.452 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.452 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.452 | |
| 2p2m | PRX | Acetyl-coenzyme A synthetase | / | 0.451 | |
| 4a6e | ASE | Acetylserotonin O-methyltransferase | 2.1.1.4 | 0.451 | |
| 4bqp | VMY | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.451 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.450 | |
| 2b55 | D31 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 2bfa | CB3 | Pteridine reductase 1 | 1.5.1.33 | 0.450 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.450 | |
| 2r8o | T5X | Transketolase 1 | / | 0.450 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.450 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.450 | |
| 5ifi | PRX | Acetyl-coenzyme A synthetase | / | 0.450 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.449 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.449 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
| 4rqu | NAD | Alcohol dehydrogenase class-P | / | 0.449 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.448 | |
| 1hnh | COA | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | / | 0.448 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.448 | |
| 3i1y | 33N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.448 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 3up3 | XCA | aceDAF-12 | / | 0.448 | |
| 5cb3 | APR | O-acetyl-ADP-ribose deacetylase | / | 0.448 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.447 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.447 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.446 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.446 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.446 | |
| 3awh | FMN | FMN-binding protein | / | 0.446 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.446 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.446 | |
| 3qu0 | X40 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.446 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.446 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.446 | |
| 1f5f | DHT | Sex hormone-binding globulin | / | 0.445 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.445 | |
| 2r8p | T6F | Transketolase 1 | / | 0.445 | |
| 3eai | 328 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.445 | |
| 3i28 | 34N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.445 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.445 | |
| 3oia | A31 | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.445 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.445 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.445 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.445 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.445 | |
| 2p0r | LEU_LEU_ACE_AR7 | Calpain-9 | / | 0.444 | |
| 2rs1 | W84 | Genome polyprotein | / | 0.444 | |
| 4dsn | GCP | GTPase KRas | / | 0.444 | |
| 4frs | 0V6 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.444 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.444 | |
| 4ol0 | GTP | GTP-binding nuclear protein Ran | / | 0.444 | |
| 4pzt | SOP | Histone acetyltransferase p300 | / | 0.444 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.444 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.444 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.443 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.443 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.443 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.443 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2x86 | ADP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.443 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.443 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.443 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.443 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.443 | |
| 4g0n | GNP | GTPase HRas | / | 0.443 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4mzu | TYD | WxcM-like protein | / | 0.443 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.443 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.443 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.442 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.442 | |
| 3bhl | THG | Thymidylate synthase | / | 0.442 | |
| 3e7i | B2 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.442 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.442 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.442 | |
| 4bcq | TJF | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 4nqg | CZH | Mitrocomin | / | 0.442 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.442 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.442 | |
| 6adh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.441 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.441 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.441 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.441 | |
| 2rgc | GNP | GTPase HRas | / | 0.441 | |
| 2vce | U2F | UDP-glycosyltransferase 72B1 | / | 0.441 | |
| 2wp9 | CBE | Succinate dehydrogenase iron-sulfur subunit | 1.3.5.1 | 0.441 | |
| 2wp9 | CBE | Succinate dehydrogenase cytochrome b556 subunit | / | 0.441 | |
| 3a6q | FMN | FMN-binding protein | / | 0.441 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 3ix3 | OHN | Transcriptional activator protein LasR | / | 0.441 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4m6p | 20R | Nicotinamide phosphoribosyltransferase | 2.4.2.12 | 0.441 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.441 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 5byl | GCP | Bifunctional AAC/APH | 2.3.1 | 0.441 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.441 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.440 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.440 | |
| 2ol4 | JPN | Enoyl-ACP reductase | / | 0.440 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.440 | |
| 3akm | 11D | Fatty acid-binding protein, intestinal | / | 0.440 | |
| 3qtz | X42 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 3up0 | D7S | aceDAF-12 | / | 0.440 | |
| 3x1z | GNP | Ras-related protein Rap-1b | / | 0.440 | |
| 4bqr | IBH | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.440 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.440 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.440 |