sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4o2r | GDP | GTP-binding protein Rheb |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4o2r | GDP | GTP-binding protein Rheb | / | 1.000 | |
| 2fe4 | GDP | Ras-related protein Rab-6B | / | 0.556 | |
| 1x1r | GDP | Ras-related protein M-Ras | / | 0.546 | |
| 4q03 | GDP | GTPase KRas | / | 0.528 | |
| 4ql3 | GDP | GTPase KRas | / | 0.518 | |
| 4epx | GDP | GTPase KRas | / | 0.516 | |
| 2fg5 | GNP | Ras-related protein Rab-31 | / | 0.511 | |
| 4lpk | GDP | GTPase KRas | / | 0.509 | |
| 4uj3 | GNP | Ras-related protein Rab-11A | / | 0.509 | |
| 1mh1 | GNP | Ras-related C3 botulinum toxin substrate 1 | / | 0.508 | |
| 3kko | GNP | Ras-related protein M-Ras | / | 0.503 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.501 | |
| 2q3f | GNP | Ras-related GTP-binding protein D | / | 0.498 | |
| 3qbt | GNP | Ras-related protein Rab-8A | / | 0.498 | |
| 4l8g | GDP | GTPase KRas | / | 0.498 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.496 | |
| 1oix | GDP | Ras-related protein Rab-11A | / | 0.494 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.492 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.489 | |
| 3cph | GDP | Ras-related protein SEC4 | / | 0.489 | |
| 2rgg | GNP | GTPase HRas | / | 0.488 | |
| 4tq9 | GDP | GTPase KRas | / | 0.487 | |
| 1z2a | GDP | Ras-related protein Rab-23 | / | 0.486 | |
| 4fid | GDP | G protein alpha subunit, putative | / | 0.486 | |
| 4l9s | GDP | GTPase HRas | / | 0.486 | |
| 3a6p | GTP | GTP-binding nuclear protein Ran | / | 0.484 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.484 | |
| 4hdq | GNP | Ras-related protein Rap-1b | / | 0.484 | |
| 4ldj | GDP | GTPase KRas | / | 0.480 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.478 | |
| 1azt | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.476 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.475 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.475 | |
| 4xvr | GNP | GTPase HRas | / | 0.475 | |
| 5c46 | GSP | Ras-related protein Rab-11A | / | 0.474 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.473 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.473 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.473 | |
| 1xtr | GNP | GTP-binding protein Rheb | / | 0.472 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.472 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1zd9 | GDP | ADP-ribosylation factor-like protein 8A | / | 0.469 | |
| 3kkq | GDP | Ras-related protein M-Ras | / | 0.469 | |
| 3tgp | GNP | GTPase HRas | / | 0.469 | |
| 3ums | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.469 | |
| 4o2l | GTP | GTP-binding protein Rheb | / | 0.469 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.468 | |
| 3wag | TYD | Glycosyltransferase | / | 0.468 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.467 | |
| 1xts | GTP | GTP-binding protein Rheb | / | 0.467 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.467 | |
| 3lbh | GNP | GTPase HRas | / | 0.466 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.466 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1zbd | GTP | Ras-related protein Rab-3A | / | 0.465 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.465 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.465 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.464 | |
| 3ddc | GNP | GTPase HRas | / | 0.464 | |
| 3pit | GNP | Ras-related protein M-Ras | / | 0.464 | |
| 4wa7 | GDP | GTPase KRas | / | 0.464 | |
| 1g16 | GDP | Ras-related protein SEC4 | / | 0.463 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.463 | |
| 3gon | ANP | Phosphomevalonate kinase | / | 0.463 | |
| 3kz1 | GSP | Transforming protein RhoA | / | 0.463 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.463 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.461 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.461 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.461 | |
| 1d5c | GDP | GTPase (Rab6) | / | 0.460 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.460 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.460 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 1zdw | FLV | Prenyltransferase | / | 0.459 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.459 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.459 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.459 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.459 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.458 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.458 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.457 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4mr9 | 2BX | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.457 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2msc | GDP | MHC class I alpha chain | / | 0.456 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.456 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 4lv6 | GDP | GTPase KRas | / | 0.456 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.456 | |
| 1dfo | PLG | Serine hydroxymethyltransferase | 2.1.2.1 | 0.455 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.455 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.455 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.455 | |
| 4epw | GDP | GTPase KRas | / | 0.455 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.455 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.454 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.454 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.454 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.454 | |
| 4l4x | NDP | AmphI | / | 0.454 | |
| 4xrb | NDP | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.454 | |
| 1xzq | FON | tRNA modification GTPase MnmE | 3.6.5 | 0.453 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.453 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.453 | |
| 4goj | GNP | ADP-ribosylation factor-like protein 3 | / | 0.453 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.453 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.452 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.452 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.452 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.452 | |
| 4giu | 636 | Anthranilate phosphoribosyltransferase | / | 0.452 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.451 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.451 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.451 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.451 | |
| 5dha | GNP | GTP-binding nuclear protein Ran | / | 0.451 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.450 | |
| 5di3 | GNP | ADP-ribosylation factor-like protein 3 | / | 0.450 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.450 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.449 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.449 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.449 | |
| 1ld7 | U66 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.448 | |
| 3c16 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.448 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.448 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.448 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.447 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.447 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.447 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.447 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.447 | |
| 5dif | GNP | GTP-binding nuclear protein Ran | / | 0.447 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.446 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.446 | |
| 1ibr | GNP | GTP-binding nuclear protein Ran | / | 0.446 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.446 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.446 | |
| 3w3z | GTP | GTP-binding nuclear protein Ran | / | 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 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.445 | |
| 2r5n | TPP | Transketolase 1 | / | 0.445 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.445 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.445 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.445 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.444 | |
| 1jcq | 739 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1ryw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.444 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 2wlf | ACO | Polysialic acid O-acetyltransferase | / | 0.444 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3t88 | S0N | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.444 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.444 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.444 | |
| 4hyv | PEP | Pyruvate kinase 1 | 2.7.1.40 | 0.444 | |
| 5c3j | UQ1 | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | / | 0.444 | |
| 5c3j | UQ1 | Succinate dehydrogenase cytochrome b560 | / | 0.444 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.443 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.443 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.443 | |
| 3ea5 | GDP | GTP-binding nuclear protein Ran | / | 0.443 | |
| 3eld | SFG | Methyltransferase | / | 0.443 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.443 | |
| 3t8w | DGZ | M17 leucyl aminopeptidase | / | 0.443 | |
| 4px9 | ADP | ATP-dependent RNA helicase DDX3X | 3.6.4.13 | 0.443 | |
| 4q02 | GDP | GTPase KRas | / | 0.443 | |
| 1i5c | ADP | Chemotaxis protein CheA | 2.7.13.3 | 0.442 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 3e6e | DCS | Alanine racemase | / | 0.442 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.441 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3gwd | NAP | Cyclohexanone monooxygenase | / | 0.441 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.441 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.441 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.441 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.441 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.441 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.440 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.440 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4obe | GDP | GTPase KRas | / | 0.440 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.440 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.440 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.440 |