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 |
|---|---|---|---|
| 3uic | 09T | Enoyl-[acyl-carrier-protein] reductase [NADH] |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3uic | 09T | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 1.000 | |
| 5cp8 | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.581 | |
| 3fnh | JPJ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.540 | |
| 2ol4 | JPN | Enoyl-ACP reductase | / | 0.537 | |
| 1zsn | TN2 | Enoyl-ACP reductase | / | 0.522 | |
| 3fnf | JPM | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.519 | |
| 4tzk | 641 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.516 | |
| 2b35 | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.514 | |
| 3nrc | TCL | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.512 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.495 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.490 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.489 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.485 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.484 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.483 | |
| 4trj | 665 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.482 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.481 | |
| 4tzt | 468 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.481 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.480 | |
| 1pox | FAD | Pyruvate oxidase | 1.2.3.3 | 0.480 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.480 | |
| 3f4b | TCL | Enoyl-acyl carrier protein reductase | / | 0.479 | |
| 3fne | 8PC | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.478 | |
| 5coq | TCU | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.478 | |
| 1p44 | GEQ | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.475 | |
| 3lsy | FT0 | Enoyl-ACP reductase | / | 0.475 | |
| 4ft0 | HK9 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.475 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.475 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.474 | |
| 2nsd | 4PI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.473 | |
| 4u0k | 744 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.473 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.472 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.472 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.471 | |
| 1zxl | JP1 | Enoyl-ACP reductase | / | 0.470 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.469 | |
| 3gbk | 2PQ | Peroxisome proliferator-activated receptor gamma | / | 0.469 | |
| 2uxu | NAR | HTH-type transcriptional regulator TtgR | / | 0.467 | |
| 3nj8 | NJ8 | Enoyl-acyl carrier reductase | / | 0.467 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.466 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.465 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.465 | |
| 2ibz | SMA | Cytochrome b | / | 0.465 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.464 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.464 | |
| 4myq | 19T | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.464 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.463 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.463 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 2w0b | CMW | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.462 | |
| 1re9 | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.461 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.461 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.461 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 3vtc | TK3 | Vitamin D3 receptor | / | 0.461 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.461 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.460 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 2op0 | 7PC | Enoyl-ACP reductase | / | 0.459 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.459 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 3oq1 | 3OQ | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 3lt1 | FT2 | Enoyl-ACP reductase | / | 0.458 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.458 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.457 | |
| 1eio | GCH | Gastrotropin | / | 0.457 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.457 | |
| 1soz | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.456 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.456 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.456 | |
| 2a5y | ATP | Cell death protein 4 | / | 0.455 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.455 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.455 | |
| 1bvr | THT | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.454 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.454 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.454 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.454 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.453 | |
| 3lt0 | FT1 | Enoyl-ACP reductase | / | 0.453 | |
| 3ox3 | 4X4 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.453 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 1fml | RTL | Retinol dehydratase | / | 0.452 | |
| 3ar6 | TG1 | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.452 | |
| 3lt2 | FT3 | Enoyl-ACP reductase | / | 0.452 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.452 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.452 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.451 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.451 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.451 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 3gwn | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.451 | |
| 3h1j | SMA | Cytochrome b | / | 0.451 | |
| 3is9 | AC7 | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.451 | |
| 1zw1 | TN5 | Enoyl-ACP reductase | / | 0.450 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.450 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.450 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.449 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.449 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.449 | |
| 3cxh | SMA | Cytochrome b | / | 0.449 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.449 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.449 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.449 | |
| 1kb9 | SMA | Cytochrome b | / | 0.448 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.448 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.448 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.448 | |
| 2gpv | OHT | Estrogen-related receptor gamma | / | 0.447 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.447 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 4iui | 1GQ | Estrogen receptor | / | 0.447 | |
| 4ybn | FAD | Flavin-nucleotide-binding protein | / | 0.447 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.446 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2o12 | FMN | Chorismate synthase | / | 0.446 | |
| 2o2s | TCL | Enoyl-acyl carrier reductase | / | 0.446 | |
| 2prh | 238 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.446 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.446 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.446 | |
| 1hk5 | T44 | Serum albumin | / | 0.445 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.445 | |
| 1kce | CB3 | Thymidylate synthase | / | 0.445 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.445 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.445 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.445 | |
| 2yiu | SMA | Cytochrome b | / | 0.445 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.445 | |
| 4knz | CB3 | Thymidylate synthase | / | 0.445 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.444 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1kvo | OAP | Phospholipase A2, membrane associated | / | 0.444 | |
| 2fgj | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.444 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3am4 | FT1 | Enoyl-ACP reductase | / | 0.444 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.443 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.443 | |
| 1xkd | NAP | Isocitrate dehydrogenase [NADP] | / | 0.443 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.443 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.443 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.443 | |
| 3irx | UDR | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.443 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.443 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.443 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.443 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.442 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.442 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.442 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.442 | |
| 3ha7 | B32 | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.442 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.442 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.442 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1dna | CB3 | Thymidylate synthase | / | 0.441 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.441 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.441 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2ejz | SAH | Diphthine synthase | / | 0.441 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 3btj | DEQ | HTH-type transcriptional regulator QacR | / | 0.441 | |
| 3l9m | L9M | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 3ol5 | SAW | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.441 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.441 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.441 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 2z78 | H86 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.440 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.440 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.440 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.440 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.440 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.440 |