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 |
|---|---|---|---|
| 4o2r | GDP | GTP-binding protein Rheb |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4o2r | GDP | GTP-binding protein Rheb | / | 1.000 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.564 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.546 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.532 | |
| 4q03 | GDP | GTPase KRas | / | 0.528 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.525 | |
| 4luc | GDP | GTPase KRas | / | 0.518 | |
| 4ql3 | GDP | GTPase KRas | / | 0.518 | |
| 4epx | GDP | GTPase KRas | / | 0.516 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.511 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.511 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.510 | |
| 4lpk | GDP | GTPase KRas | / | 0.510 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.508 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.506 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.503 | |
| 4qxa | GTP | Ras-related protein Rab-9A | / | 0.500 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.498 | |
| 4l8g | GDP | GTPase KRas | / | 0.498 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.496 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.492 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.490 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.489 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.488 | |
| 2rgg | GNP | GTPase HRas | / | 0.488 | |
| 4tq9 | GDP | GTPase KRas | / | 0.487 | |
| 1z0a | GDP | Ras-related protein Rab-2A | / | 0.486 | |
| 4l9s | GDP | GTPase HRas | / | 0.486 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.485 | |
| 2xtz | GSP | Guanine nucleotide-binding protein alpha-1 subunit | / | 0.484 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.484 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.484 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.483 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.481 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.481 | |
| 3wag | TYD | Glycosyltransferase | / | 0.480 | |
| 4ldj | GDP | GTPase KRas | / | 0.480 | |
| 4lhw | GNP | Ras-related protein Rab-8A | / | 0.480 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.479 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.478 | |
| 1uad | GNP | Ras-related protein Ral-A | / | 0.477 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.476 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.476 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.476 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.475 | |
| 4xvr | GNP | GTPase HRas | / | 0.475 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.473 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.472 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.472 | |
| 4px9 | ADP | ATP-dependent RNA helicase DDX3X | 3.6.4.13 | 0.472 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.471 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.471 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.470 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.469 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.469 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.469 | |
| 3tgp | GNP | GTPase HRas | / | 0.469 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.469 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.468 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.467 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.467 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.466 | |
| 3lbh | GNP | GTPase HRas | / | 0.466 | |
| 3ddc | GNP | GTPase HRas | / | 0.464 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.464 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.464 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.464 | |
| 4wa7 | GDP | GTPase KRas | / | 0.464 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.463 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.463 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.461 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.461 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.461 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.461 | |
| 4d0l | GSP | Ras-related protein Rab-11A | / | 0.461 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.461 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.460 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.460 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.460 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 3nbz | GTP | GTP-binding nuclear protein Ran | / | 0.459 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.458 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.458 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.458 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.457 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.456 | |
| 4lv6 | GDP | GTPase KRas | / | 0.456 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.455 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.455 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.455 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.455 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.455 | |
| 2gil | GTP | Ras-related protein Rab-6A | / | 0.455 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.455 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.455 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.455 | |
| 4epw | GDP | GTPase KRas | / | 0.455 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.455 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 1jcq | 739 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.454 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 1yhn | GTP | Ras-related protein Rab-7a | / | 0.454 | |
| 4uj5 | GNP | Ras-related protein Rab-11A | / | 0.454 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.453 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.453 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.453 | |
| 4i42 | 1HA | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.453 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.453 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.453 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.452 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.452 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.452 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.451 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.451 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.451 | |
| 4h30 | 0ZD | Macrophage metalloelastase | 3.4.24.65 | 0.451 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.450 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.450 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 0.450 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.450 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.450 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.450 | |
| 4r7u | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.450 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.450 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.450 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.449 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.449 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.448 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.448 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.448 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.448 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.448 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.447 | |
| 1ld7 | U66 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.447 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.447 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.447 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.447 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.447 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.447 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.447 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3e5h | GNP | Ras-related protein Rab-28 | / | 0.446 | |
| 4cid | ANP | EH domain-containing protein 2 | / | 0.446 | |
| 4f4q | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.446 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.446 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.446 | |
| 1ryw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.445 | |
| 1tu3 | GNP | Ras-related protein Rab-5A | / | 0.445 | |
| 2d1c | NAP | Isocitrate dehydrogenase [NADP] | 1.1.1.42 | 0.445 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.445 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.445 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 4fry | NAD | Putative signal-transduction protein with CBS domains | / | 0.445 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.445 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.444 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.444 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 2xq0 | BES | Leukotriene A-4 hydrolase homolog | 3.3.2.6 | 0.444 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.444 | |
| 3eld | SFG | Methyltransferase | / | 0.444 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3t88 | S0N | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.444 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.444 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.443 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.443 | |
| 3bhr | THG | Thymidylate synthase | / | 0.443 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.443 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.443 | |
| 3t8w | DGZ | M17 leucyl aminopeptidase | / | 0.443 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.443 | |
| 4q02 | GDP | GTPase KRas | / | 0.443 | |
| 5cfp | C2E | Stimulator of interferon genes protein | / | 0.443 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.442 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.442 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.442 | |
| 1xu7 | CPS | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 2gz7 | D3F | Orf1a polyprotein | / | 0.442 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.442 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.442 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.442 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.441 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.441 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.441 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.441 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.441 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.441 | |
| 1a4r | GNH | Cell division control protein 42 homolog | / | 0.440 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.440 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.440 | |
| 4hx5 | 19V | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4obe | GDP | GTPase KRas | / | 0.440 |