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 |
|---|---|---|---|
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 1.000 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.598 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.590 | |
| 1upa | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.566 | |
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.560 | |
| 1upb | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.553 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.518 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.504 | |
| 2pan | TDP | Glyoxylate carboligase | 4.1.1.47 | 0.502 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.500 | |
| 2c3o | TPP | Pyruvate synthase | / | 0.497 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.496 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.489 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.487 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.486 | |
| 4l8u | 9AZ | Serum albumin | / | 0.483 | |
| 2ag0 | TPP | Benzaldehyde lyase | / | 0.481 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.478 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.478 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.477 | |
| 2q5q | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.477 | |
| 1kek | HTL | Pyruvate synthase | / | 0.475 | |
| 2uz1 | TPP | Benzaldehyde lyase | / | 0.474 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.474 | |
| 2pda | TPP | Pyruvate synthase | / | 0.473 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 1vjy | 460 | TGF-beta receptor type-1 | 2.7.11.30 | 0.469 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.467 | |
| 2uza | HTL | Pyruvate synthase | / | 0.466 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 2c3u | 2TP | Pyruvate synthase | / | 0.465 | |
| 4u07 | ATP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.465 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.463 | |
| 2c3y | HTL | Pyruvate synthase | / | 0.462 | |
| 5ej7 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.462 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.461 | |
| 4y1b | NAP | AntE | / | 0.461 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.461 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.459 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.459 | |
| 4eh8 | IRG | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.458 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.458 | |
| 3r95 | ACO | MccE protein | / | 0.457 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.457 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.457 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.456 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.456 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 2r5n | TPP | Transketolase 1 | / | 0.455 | |
| 3oe1 | TDL | Pyruvate decarboxylase | 4.1.1.1 | 0.455 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 5eso | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.455 | |
| 2dwb | ANP | Aurora kinase A | 2.7.11.1 | 0.454 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.454 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.454 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.454 | |
| 1ppj | ANY | Cytochrome b | / | 0.453 | |
| 1qpb | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.453 | |
| 2c31 | TZD | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.453 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.453 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.453 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.453 | |
| 5esd | TDP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.453 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.452 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.451 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.451 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.451 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.451 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.450 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.450 | |
| 2ji6 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.450 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.449 | |
| 3gds | VAL_TYR_TYR_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.449 | |
| 3hwx | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.449 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.449 | |
| 4eh3 | IRG | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.448 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.448 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.448 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1bmf | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.447 | |
| 1bmf | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.447 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.447 | |
| 3vmm | P0D | Alanine--anticapsin ligase | / | 0.447 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.446 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.446 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.446 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.446 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.446 | |
| 3r2b | 05B | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.446 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.446 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.446 | |
| 5eja | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.446 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.445 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.445 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4zth | GG5 | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 5ebu | FMN | Lactate oxidase | / | 0.445 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.445 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.444 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 3r0t | FU9 | Casein kinase II subunit alpha | 2.7.11.1 | 0.444 | |
| 4im0 | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.444 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.444 | |
| 1zdw | FLV | Prenyltransferase | / | 0.443 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.443 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.442 | |
| 4cgd | 8P3 | Integrase | / | 0.442 | |
| 4tlx | FDA | KtzI | / | 0.442 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.442 | |
| 5iqf | GDP | Bifunctional AAC/APH | 2.3.1 | 0.442 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.441 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.441 | |
| 1pvd | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.441 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.441 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.441 | |
| 3mje | NDP | AmphB | / | 0.441 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3x0a | 5GP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.441 | |
| 4mpp | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 2g0g | SP0 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.440 | |
| 2mm3 | CHO | Gastrotropin | / | 0.440 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2ybo | SAH | Methyltransferase | / | 0.440 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3ln1 | CEL | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.440 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 3rdq | DTB | Streptavidin | / | 0.440 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.440 |