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 |
|---|---|---|---|
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 1.000 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.706 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.706 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.667 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.649 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.647 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.602 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.572 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.566 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.564 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.561 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.532 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.530 | |
| 1b8n | IMG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.526 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.518 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.516 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.503 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.501 | |
| 1rct | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.499 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.497 | |
| 1b8o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.496 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.493 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.489 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.488 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.487 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.482 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.481 | |
| 1a9s | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.478 | |
| 1v45 | 3DG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.477 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.477 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.476 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.475 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.474 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.470 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.469 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 3v2u | ATP | Protein GAL3 | / | 0.467 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 2ejz | SAH | Diphthine synthase | / | 0.466 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.466 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.466 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.464 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.463 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1pf7 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.459 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.459 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.459 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.458 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3qbj | NXZ | Dipeptidyl peptidase 4 | / | 0.458 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.457 | |
| 2dvo | ITT | dITP/XTP pyrophosphatase | 3.6.1.19 | 0.457 | |
| 4jic | FMN | GTN Reductase | / | 0.457 | |
| 1l2t | ATP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.456 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.456 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.455 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.452 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.452 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.452 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.452 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.451 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.450 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 5czy | SAM | Eukaryotic huntingtin interacting protein B | / | 0.450 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.449 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.449 | |
| 5dp2 | NAP | CurF | / | 0.449 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.448 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 1lv8 | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.447 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.447 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.447 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3f8w | ADN | Purine nucleoside phosphorylase | / | 0.447 | |
| 4j7h | TRH | PCZA361.3 | / | 0.447 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.446 | |
| 4y1b | NAP | AntE | / | 0.446 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.445 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.445 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.445 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.445 | |
| 4e2b | FMN | Dehydrogenase | / | 0.445 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.444 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.443 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.443 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.443 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.443 | |
| 3qls | 55V | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4dja | FAD | (6-4) photolyase | / | 0.443 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.441 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.441 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.440 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.440 | |
| 3r95 | ACO | MccE protein | / | 0.440 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.440 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3zec | ANP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.440 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.440 |