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 |
|---|---|---|---|
| 2huv | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2huv | SAH | Diphthine synthase | / | 1.000 | |
| 2owg | SAH | Diphthine synthase | / | 0.866 | |
| 2e4n | SAH | Diphthine synthase | / | 0.823 | |
| 2p9d | SAH | Diphthine synthase | / | 0.816 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.805 | |
| 2pca | SAH | Diphthine synthase | / | 0.801 | |
| 2el3 | SAH | Diphthine synthase | / | 0.792 | |
| 2e8r | SAH | Diphthine synthase | / | 0.790 | |
| 2huq | SAH | Diphthine synthase | / | 0.790 | |
| 2eld | SAH | Diphthine synthase | / | 0.763 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.762 | |
| 2e07 | SAH | Diphthine synthase | / | 0.755 | |
| 1wng | SAH | Diphthine synthase | / | 0.746 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.742 | |
| 2owk | SAH | Diphthine synthase | / | 0.727 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.724 | |
| 2el0 | SAH | Diphthine synthase | / | 0.723 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.721 | |
| 2dxx | SAH | Diphthine synthase | / | 0.716 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.715 | |
| 2z6r | SAH | Diphthine synthase | / | 0.713 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.712 | |
| 2p6i | SAH | Diphthine synthase | / | 0.712 | |
| 2ele | SAH | Diphthine synthase | / | 0.705 | |
| 2p5c | SAH | Diphthine synthase | / | 0.703 | |
| 2ejj | SAH | Diphthine synthase | / | 0.702 | |
| 2p5f | SAH | Diphthine synthase | / | 0.700 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.694 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.694 | |
| 2pck | SAH | Diphthine synthase | / | 0.694 | |
| 2hut | SAH | Diphthine synthase | / | 0.688 | |
| 2e17 | SAH | Diphthine synthase | / | 0.681 | |
| 2e15 | SAH | Diphthine synthase | / | 0.679 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.679 | |
| 2pch | SAH | Diphthine synthase | / | 0.679 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.673 | |
| 2e7r | SAH | Diphthine synthase | / | 0.673 | |
| 2dsh | SAH | Diphthine synthase | / | 0.672 | |
| 2hux | SAH | Diphthine synthase | / | 0.671 | |
| 2pcg | SAH | Diphthine synthase | / | 0.661 | |
| 2dsi | SAH | Diphthine synthase | / | 0.659 | |
| 2ehl | SAH | Diphthine synthase | / | 0.657 | |
| 1vce | SAH | Diphthine synthase | / | 0.654 | |
| 2emr | SAH | Diphthine synthase | / | 0.653 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.652 | |
| 2eni | SAH | Diphthine synthase | / | 0.651 | |
| 2e8q | SAH | Diphthine synthase | / | 0.649 | |
| 2dxw | SAH | Diphthine synthase | / | 0.645 | |
| 2dsg | SAH | Diphthine synthase | / | 0.642 | |
| 2p2x | SAH | Diphthine synthase | / | 0.641 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.639 | |
| 2p6k | SAH | Diphthine synthase | / | 0.637 | |
| 2ejk | SAH | Diphthine synthase | / | 0.635 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.635 | |
| 2emu | SAH | Diphthine synthase | / | 0.634 | |
| 2dxv | SAH | Diphthine synthase | / | 0.631 | |
| 2owu | SAH | Diphthine synthase | / | 0.628 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.626 | |
| 2p6d | SAH | Diphthine synthase | / | 0.626 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.626 | |
| 2pci | SAH | Diphthine synthase | / | 0.621 | |
| 2en5 | SAH | Diphthine synthase | / | 0.618 | |
| 2pcm | SAH | Diphthine synthase | / | 0.618 | |
| 2eeq | SAH | Diphthine synthase | / | 0.616 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.613 | |
| 2eka | SAH | Diphthine synthase | / | 0.611 | |
| 2egs | SAH | Diphthine synthase | / | 0.609 | |
| 2e8s | SAH | Diphthine synthase | / | 0.606 | |
| 2e08 | SAH | Diphthine synthase | / | 0.589 | |
| 2e16 | SAH | Diphthine synthase | / | 0.583 | |
| 2p6l | SAH | Diphthine synthase | / | 0.581 | |
| 2ejz | SAH | Diphthine synthase | / | 0.575 | |
| 2egb | SAH | Diphthine synthase | / | 0.573 | |
| 2egl | SAH | Diphthine synthase | / | 0.566 | |
| 2dek | SAH | Diphthine synthase | / | 0.564 | |
| 2e8h | SAH | Diphthine synthase | / | 0.556 | |
| 2owv | SAH | Diphthine synthase | / | 0.550 | |
| 2owf | SAH | Diphthine synthase | / | 0.545 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.504 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.480 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.479 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.478 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.475 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.474 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.473 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.473 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.471 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.468 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.467 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.467 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.467 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.467 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.466 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.466 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.464 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.464 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.462 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.461 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.461 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.461 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.460 | |
| 2cgv | 3B3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.460 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.460 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.459 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.458 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.458 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.457 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.457 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.456 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.456 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.455 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.455 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.455 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.454 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.454 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.454 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.454 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.454 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.453 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.453 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.453 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.453 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.451 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.451 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.451 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.450 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.450 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.449 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.449 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.449 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.449 | |
| 5dp2 | NAP | CurF | / | 0.449 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.448 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.448 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.447 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.447 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.447 | |
| 2w06 | FRV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.447 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.447 | |
| 3p2e | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.447 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.447 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.446 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.446 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.446 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.446 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.445 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.445 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.445 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.445 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.445 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.445 | |
| 3rai | X85 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.444 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.444 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.444 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.444 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.444 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1kor | ANP | Argininosuccinate synthase | / | 0.443 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.443 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.443 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.442 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.442 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.442 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.442 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.442 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.442 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.442 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.442 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.442 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.441 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.441 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.441 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.441 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.441 | |
| 2hrc | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.441 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.441 | |
| 2y3s | TIR | TamL | / | 0.441 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.441 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.440 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.440 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.440 | |
| 2xvu | 9DN | Serum albumin | / | 0.440 | |
| 3a3g | DLZ | Lumazine protein | / | 0.440 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 |