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 |
|---|---|---|---|
| 2p6i | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2p6i | SAH | Diphthine synthase | / | 1.000 | |
| 2p5c | SAH | Diphthine synthase | / | 0.844 | |
| 2pck | SAH | Diphthine synthase | / | 0.831 | |
| 2dxx | SAH | Diphthine synthase | / | 0.828 | |
| 2e08 | SAH | Diphthine synthase | / | 0.820 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.815 | |
| 2e7r | SAH | Diphthine synthase | / | 0.800 | |
| 2dsi | SAH | Diphthine synthase | / | 0.799 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.782 | |
| 2eeq | SAH | Diphthine synthase | / | 0.779 | |
| 2owu | SAH | Diphthine synthase | / | 0.777 | |
| 2p9d | SAH | Diphthine synthase | / | 0.757 | |
| 2owg | SAH | Diphthine synthase | / | 0.755 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.752 | |
| 2eni | SAH | Diphthine synthase | / | 0.752 | |
| 2ejk | SAH | Diphthine synthase | / | 0.744 | |
| 2egb | SAH | Diphthine synthase | / | 0.740 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.737 | |
| 2huq | SAH | Diphthine synthase | / | 0.733 | |
| 2pcg | SAH | Diphthine synthase | / | 0.733 | |
| 2dsh | SAH | Diphthine synthase | / | 0.730 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.729 | |
| 2e15 | SAH | Diphthine synthase | / | 0.727 | |
| 2p5f | SAH | Diphthine synthase | / | 0.727 | |
| 2hut | SAH | Diphthine synthase | / | 0.725 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.722 | |
| 2e8h | SAH | Diphthine synthase | / | 0.719 | |
| 2huv | SAH | Diphthine synthase | / | 0.717 | |
| 2e17 | SAH | Diphthine synthase | / | 0.709 | |
| 2owk | SAH | Diphthine synthase | / | 0.708 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.699 | |
| 2pca | SAH | Diphthine synthase | / | 0.698 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.696 | |
| 2pch | SAH | Diphthine synthase | / | 0.696 | |
| 2e07 | SAH | Diphthine synthase | / | 0.695 | |
| 2p6k | SAH | Diphthine synthase | / | 0.690 | |
| 2ejj | SAH | Diphthine synthase | / | 0.686 | |
| 2dsg | SAH | Diphthine synthase | / | 0.679 | |
| 2egs | SAH | Diphthine synthase | / | 0.675 | |
| 2eld | SAH | Diphthine synthase | / | 0.674 | |
| 2dxv | SAH | Diphthine synthase | / | 0.673 | |
| 2p2x | SAH | Diphthine synthase | / | 0.672 | |
| 2z6r | SAH | Diphthine synthase | / | 0.668 | |
| 2dxw | SAH | Diphthine synthase | / | 0.666 | |
| 2owv | SAH | Diphthine synthase | / | 0.664 | |
| 2ele | SAH | Diphthine synthase | / | 0.660 | |
| 1wng | SAH | Diphthine synthase | / | 0.658 | |
| 2el3 | SAH | Diphthine synthase | / | 0.658 | |
| 2emr | SAH | Diphthine synthase | / | 0.658 | |
| 2p6d | SAH | Diphthine synthase | / | 0.656 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.655 | |
| 1vce | SAH | Diphthine synthase | / | 0.651 | |
| 2pci | SAH | Diphthine synthase | / | 0.651 | |
| 2emu | SAH | Diphthine synthase | / | 0.650 | |
| 2e8r | SAH | Diphthine synthase | / | 0.645 | |
| 2eka | SAH | Diphthine synthase | / | 0.645 | |
| 2ehl | SAH | Diphthine synthase | / | 0.642 | |
| 2e4n | SAH | Diphthine synthase | / | 0.635 | |
| 2el0 | SAH | Diphthine synthase | / | 0.635 | |
| 2e8s | SAH | Diphthine synthase | / | 0.634 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.630 | |
| 2dek | SAH | Diphthine synthase | / | 0.629 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.629 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.625 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.615 | |
| 2hux | SAH | Diphthine synthase | / | 0.615 | |
| 2pcm | SAH | Diphthine synthase | / | 0.614 | |
| 2egl | SAH | Diphthine synthase | / | 0.611 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.603 | |
| 2owf | SAH | Diphthine synthase | / | 0.596 | |
| 2e8q | SAH | Diphthine synthase | / | 0.591 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.579 | |
| 2p6l | SAH | Diphthine synthase | / | 0.570 | |
| 2ejz | SAH | Diphthine synthase | / | 0.564 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.564 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.554 | |
| 2e16 | SAH | Diphthine synthase | / | 0.537 | |
| 2en5 | SAH | Diphthine synthase | / | 0.536 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.505 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.504 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.493 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.488 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.484 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.484 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.481 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.480 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.477 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.477 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.476 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.474 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.473 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.473 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.472 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 2y3s | TIR | TamL | / | 0.470 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.470 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.469 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.468 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.467 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.466 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.465 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.464 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.464 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.464 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.464 | |
| 1bmf | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.463 | |
| 1bmf | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.463 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.463 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.463 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.461 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.460 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.460 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.460 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.459 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.458 | |
| 3rai | X85 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.458 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.457 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.457 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.457 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.456 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.456 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.456 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.456 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.455 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.454 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.454 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.454 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.453 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.453 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.453 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.453 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.453 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.453 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.453 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.453 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.452 | |
| 2v7q | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.452 | |
| 2v7q | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.452 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.451 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.451 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.451 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.451 | |
| 3wb2 | YGP | Uncharacterized protein MJ0488 | / | 0.451 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.451 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 1civ | NAP | Malate dehydrogenase [NADP], chloroplastic | 1.1.1.82 | 0.450 | |
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.450 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.450 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.450 | |
| 2cgv | 3B3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.450 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.450 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.449 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.449 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.449 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.449 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.449 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.449 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.449 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.448 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.448 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.447 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.447 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.447 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.447 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.447 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.447 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.446 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.446 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.446 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.446 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.446 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.446 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.446 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.446 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.445 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.445 | |
| 3kgc | LY7 | Glutamate receptor 2 | / | 0.445 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.445 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.445 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.444 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.444 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.443 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.443 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2a87 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.442 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.442 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.442 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.442 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.442 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.441 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.441 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.441 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3q3c | NAD | NAD-dependent L-serine dehydrogenase | / | 0.441 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.441 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.441 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.441 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.441 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.441 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.440 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.440 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.440 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.440 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3so9 | 017 | Pol protein | / | 0.440 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.440 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.440 |