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 |
|---|---|---|---|
| 2p5y | NAD | UDP-glucose 4-epimerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 1.000 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.494 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.494 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.493 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.487 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.482 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.479 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.479 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.479 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.478 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.477 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.474 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.474 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.473 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.473 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.471 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.471 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.470 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.470 | |
| 1lqu | NDP | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.469 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.469 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.468 | |
| 1c3e | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.467 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.467 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.466 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.465 | |
| 3uqd | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.465 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 1c2t | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.463 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.462 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.462 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 4z0g | 5GP | Inosine-5'-monophosphate dehydrogenase | / | 0.460 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.460 | |
| 1ek5 | NAD | UDP-glucose 4-epimerase | / | 0.459 | |
| 1gqt | ACP | Ribokinase | / | 0.459 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.459 | |
| 2vtt | LZD | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.459 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.459 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.459 | |
| 1snu | STU | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.458 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.458 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.458 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.457 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.457 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.457 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.457 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.457 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.456 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.456 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.456 | |
| 3tki | S25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.456 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.456 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.455 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.455 | |
| 2e8h | SAH | Diphthine synthase | / | 0.455 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.455 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.455 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.455 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.455 | |
| 4a4q | UX9 | Pol protein | / | 0.455 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.455 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.455 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.455 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.454 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.454 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.454 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.454 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.454 | |
| 4rqk | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.454 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.453 | |
| 2rl1 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.453 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.452 | |
| 2qfx | NDP | Isocitrate dehydrogenase [NADP], mitochondrial | 1.1.1.42 | 0.452 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.452 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.452 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2emr | SAH | Diphthine synthase | / | 0.451 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.451 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3dog | NNN | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3o99 | K13 | Pol polyprotein | / | 0.451 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.451 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.450 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.450 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.450 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.450 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.450 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.450 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.449 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.449 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.449 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 3t8v | BTJ | M1 family aminopeptidase | 3.4.11 | 0.449 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.449 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.449 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.448 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.448 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.448 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 2xrw | ANP | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.448 | |
| 3lpb | NVB | Tyrosine-protein kinase JAK2 | / | 0.448 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.448 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.448 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 1bxq | PP8 | Penicillopepsin-1 | 3.4.23.20 | 0.447 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.447 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.447 | |
| 1wng | SAH | Diphthine synthase | / | 0.447 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.447 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.447 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.447 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 3sw1 | FMN | Sensory box protein | / | 0.447 | |
| 4ig0 | 1FG | Gag-Pol polyprotein | 2.7.7.49 | 0.447 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.447 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.447 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.447 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.446 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.446 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.446 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.446 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 5doz | NDP | JamJ | / | 0.446 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.445 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.445 | |
| 2el0 | SAH | Diphthine synthase | / | 0.445 | |
| 2hux | SAH | Diphthine synthase | / | 0.445 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.445 | |
| 2qo7 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.445 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.445 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.445 | |
| 3elu | SAM | Methyltransferase | / | 0.445 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.445 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.445 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.445 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.445 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.445 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.445 | |
| 4iva | 1J5 | Tyrosine-protein kinase JAK2 | / | 0.445 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.445 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.444 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.444 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.444 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.444 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.444 | |
| 4gk4 | L90 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
| 4qna | X11 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.444 | |
| 1qpd | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.443 | |
| 2emu | SAH | Diphthine synthase | / | 0.443 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.443 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.443 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 3lzu | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3ruv | ANP | Chaperonin | / | 0.443 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.443 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.443 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.443 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.443 | |
| 1cde | GAR | Phosphoribosylglycinamide formyltransferase | / | 0.442 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.442 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.442 | |
| 1sgu | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2e07 | SAH | Diphthine synthase | / | 0.442 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.442 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.442 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.442 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.442 | |
| 3eyh | IZA | Tyrosine-protein kinase JAK1 | / | 0.442 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.442 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.442 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.442 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1eh4 | IC1 | Casein kinase I homolog 1 | 2.7.11.1 | 0.441 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.441 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.441 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.441 | |
| 3anm | SYD | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.441 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.441 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.441 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.441 | |
| 3qbd | NAD | 3-dehydroquinate synthase | 4.2.3.4 | 0.441 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3v5l | 0G1 | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.441 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.441 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 4ft7 | H3K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.441 | |
| 4kip | 1R9 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.441 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2dsi | SAH | Diphthine synthase | / | 0.440 | |
| 2huv | SAH | Diphthine synthase | / | 0.440 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.440 | |
| 3iaa | TYD | CalG2 | / | 0.440 | |
| 3tza | TZG | Glutamate receptor 2 | / | 0.440 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 4dqf | 017 | Gag-Pol polyprotein | / | 0.440 | |
| 4fv8 | E63 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 5a3b | APR | SIR2 family protein | / | 0.440 | |
| 5cyo | GDP | Septin-9 | / | 0.440 |