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 |
|---|---|---|---|
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 1.000 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.811 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.713 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.696 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.671 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.658 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.620 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.602 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.586 | |
| 1b8o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.558 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.554 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.547 | |
| 1a9s | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.546 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.538 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.531 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.517 | |
| 3ggs | 2FD | Purine nucleoside phosphorylase | 2.4.2.1 | 0.517 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.513 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.510 | |
| 1rct | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.506 | |
| 1b8n | IMG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.502 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.502 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.490 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.490 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.488 | |
| 5dp2 | NAP | CurF | / | 0.485 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.484 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.482 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.481 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.481 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.481 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.481 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.479 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.478 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.474 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.471 | |
| 3f8w | ADN | Purine nucleoside phosphorylase | / | 0.471 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.471 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.470 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.469 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.468 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.468 | |
| 1v45 | 3DG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.468 | |
| 2ejz | SAH | Diphthine synthase | / | 0.467 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 1pf7 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.466 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.466 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.466 | |
| 3wag | TYD | Glycosyltransferase | / | 0.466 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.465 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.465 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.464 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.463 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 3v2u | ATP | Protein GAL3 | / | 0.463 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.462 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.462 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.462 | |
| 4e2b | FMN | Dehydrogenase | / | 0.462 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.461 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.461 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.460 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.460 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.460 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.459 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.459 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.458 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.458 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.458 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.458 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.458 | |
| 1lv8 | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.457 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.457 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.455 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.454 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.454 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.453 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.452 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.452 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.452 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 1m8h | 6NI | Nitric oxide synthase, inducible | 1.14.13.39 | 0.451 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.451 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3w2f | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.451 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.451 | |
| 4y1b | NAP | AntE | / | 0.451 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.450 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.450 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.450 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4jic | FMN | GTN Reductase | / | 0.450 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.449 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.449 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.449 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.449 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.449 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.449 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1oj4 | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.448 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.448 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.448 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.448 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 5bnw | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.448 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.447 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.447 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.446 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.446 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.445 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.445 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.444 | |
| 3ox4 | NAD | Alcohol dehydrogenase 2 | 1.1.1.1 | 0.444 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.444 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.444 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4er6 | AW2 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.444 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.444 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.444 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.443 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.443 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1sd1 | FMC | S-methyl-5'-thioadenosine phosphorylase | / | 0.443 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2dvo | ITT | dITP/XTP pyrophosphatase | 3.6.1.19 | 0.443 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.443 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.443 | |
| 2qe2 | 452 | Polyprotein | / | 0.443 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.443 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.443 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.442 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.442 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 4gi2 | NAP | Crotonyl-CoA carboxylase/reductase | / | 0.442 | |
| 4usq | FAD | Pyridine nucleotide-disulfide oxidoreductase | / | 0.442 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.441 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.440 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.440 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.440 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.440 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.440 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.440 |