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 |
|---|---|---|---|
| 2ehl | SAH | Diphthine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ehl | SAH | Diphthine synthase | / | 1.000 | |
| 2emr | SAH | Diphthine synthase | / | 0.863 | |
| 2p6d | SAH | Diphthine synthase | / | 0.844 | |
| 2owk | SAH | Diphthine synthase | / | 0.843 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.825 | |
| 2ele | SAH | Diphthine synthase | / | 0.825 | |
| 2emu | SAH | Diphthine synthase | / | 0.817 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.812 | |
| 2eni | SAH | Diphthine synthase | / | 0.794 | |
| 2dxv | SAH | Diphthine synthase | / | 0.789 | |
| 2pcm | SAH | Diphthine synthase | / | 0.784 | |
| 2dxw | SAH | Diphthine synthase | / | 0.774 | |
| 2e8s | SAH | Diphthine synthase | / | 0.771 | |
| 2eka | SAH | Diphthine synthase | / | 0.768 | |
| 2ejk | SAH | Diphthine synthase | / | 0.763 | |
| 2e8r | SAH | Diphthine synthase | / | 0.758 | |
| 2hut | SAH | Diphthine synthase | / | 0.750 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.747 | |
| 2e7r | SAH | Diphthine synthase | / | 0.743 | |
| 2dsg | SAH | Diphthine synthase | / | 0.732 | |
| 2pcg | SAH | Diphthine synthase | / | 0.727 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.723 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.718 | |
| 2p6k | SAH | Diphthine synthase | / | 0.713 | |
| 2egb | SAH | Diphthine synthase | / | 0.712 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.702 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.702 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.702 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.702 | |
| 2egs | SAH | Diphthine synthase | / | 0.699 | |
| 2p5f | SAH | Diphthine synthase | / | 0.696 | |
| 2e8q | SAH | Diphthine synthase | / | 0.694 | |
| 2egl | SAH | Diphthine synthase | / | 0.694 | |
| 2el3 | SAH | Diphthine synthase | / | 0.689 | |
| 2e16 | SAH | Diphthine synthase | / | 0.686 | |
| 2e4n | SAH | Diphthine synthase | / | 0.683 | |
| 2en5 | SAH | Diphthine synthase | / | 0.683 | |
| 2p5c | SAH | Diphthine synthase | / | 0.683 | |
| 2eld | SAH | Diphthine synthase | / | 0.682 | |
| 2owg | SAH | Diphthine synthase | / | 0.674 | |
| 2hux | SAH | Diphthine synthase | / | 0.669 | |
| 2p2x | SAH | Diphthine synthase | / | 0.669 | |
| 2dxx | SAH | Diphthine synthase | / | 0.668 | |
| 2ek3 | SAH | Diphthine synthase | / | 0.668 | |
| 2pck | SAH | Diphthine synthase | / | 0.668 | |
| 1vce | SAH | Diphthine synthase | / | 0.658 | |
| 2e08 | SAH | Diphthine synthase | / | 0.658 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.658 | |
| 2dsi | SAH | Diphthine synthase | / | 0.657 | |
| 2huv | SAH | Diphthine synthase | / | 0.656 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.647 | |
| 2pch | SAH | Diphthine synthase | / | 0.647 | |
| 2e8h | SAH | Diphthine synthase | / | 0.646 | |
| 2owv | SAH | Diphthine synthase | / | 0.646 | |
| 2e17 | SAH | Diphthine synthase | / | 0.645 | |
| 2e15 | SAH | Diphthine synthase | / | 0.642 | |
| 2pb5 | SAH | Diphthine synthase | / | 0.642 | |
| 2el0 | SAH | Diphthine synthase | / | 0.639 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.636 | |
| 2p6i | SAH | Diphthine synthase | / | 0.634 | |
| 2z6r | SAH | Diphthine synthase | / | 0.634 | |
| 2dek | SAH | Diphthine synthase | / | 0.631 | |
| 2pci | SAH | Diphthine synthase | / | 0.626 | |
| 1wng | SAH | Diphthine synthase | / | 0.625 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.618 | |
| 2owu | SAH | Diphthine synthase | / | 0.608 | |
| 2p9d | SAH | Diphthine synthase | / | 0.605 | |
| 2huq | SAH | Diphthine synthase | / | 0.595 | |
| 2p6l | SAH | Diphthine synthase | / | 0.591 | |
| 2pca | SAH | Diphthine synthase | / | 0.589 | |
| 2owf | SAH | Diphthine synthase | / | 0.588 | |
| 2ejz | SAH | Diphthine synthase | / | 0.586 | |
| 2eeq | SAH | Diphthine synthase | / | 0.580 | |
| 2e07 | SAH | Diphthine synthase | / | 0.567 | |
| 2eh4 | SAH | Diphthine synthase | / | 0.561 | |
| 2ejj | SAH | Diphthine synthase | / | 0.523 | |
| 2dsh | SAH | Diphthine synthase | / | 0.518 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.495 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.491 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.488 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.484 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.483 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.481 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.479 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.478 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.476 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.474 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.473 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.473 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.473 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.472 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.470 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.469 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.467 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 4dx9 | SER_ALA_VAL_THR | Integrin beta-1 | / | 0.465 | |
| 4dx9 | SER_ALA_VAL_THR | Integrin beta-1-binding protein 1 | / | 0.465 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.464 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.464 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.463 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.463 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.463 | |
| 2y3s | TIR | TamL | / | 0.463 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.463 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.462 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.462 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.460 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.459 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.457 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.457 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.456 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.455 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.455 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.454 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.454 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.454 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.454 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.453 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.453 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.453 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.453 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.453 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.453 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.452 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.452 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.452 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.452 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.452 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.451 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.451 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.451 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.450 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.450 | |
| 1h8h | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.449 | |
| 1h8h | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.449 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.449 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.449 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.449 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.449 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 4xr9 | NAD | CalS8 | / | 0.449 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.448 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.448 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 2xx9 | 1NF | Glutamate receptor 2 | / | 0.447 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.447 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.447 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.446 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.446 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.446 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.446 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1j1z | ATP | Argininosuccinate synthase | / | 0.445 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1kor | ANP | Argininosuccinate synthase | / | 0.445 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.445 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2jcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.445 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.445 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.445 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.445 | |
| 3a3g | DLZ | Lumazine protein | / | 0.445 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.445 | |
| 4irn | FAD | AnaB | / | 0.445 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.444 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.444 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 2fgj | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.444 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.444 | |
| 1e1q | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1e1q | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3u9e | COA | Lmo1369 protein | / | 0.443 | |
| 3vn2 | TLS | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.443 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.442 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1zio | AP5 | Adenylate kinase | / | 0.442 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.442 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.442 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.442 | |
| 2y3r | TRK | TamL | / | 0.441 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.441 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.440 | |
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 1z1f | STL | Resveratrol synthase | / | 0.440 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.440 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.440 | |
| 2z3l | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.440 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 |