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 |
|---|---|---|---|
| 4mpp | TZD | Benzoylformate decarboxylase | 4.1.1.7 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4mpp | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 1.000 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.607 | |
| 4jub | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.597 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.591 | |
| 4ju9 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.583 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.566 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.561 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.533 | |
| 1po7 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.519 | |
| 4ju8 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.517 | |
| 4juc | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.514 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.509 | |
| 4mpr | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.507 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.485 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.481 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.481 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.478 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.478 | |
| 4gm4 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.476 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.474 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.474 | |
| 3nwz | COA | BH2602 protein | / | 0.472 | |
| 1bfd | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.471 | |
| 1uym | PU3 | Heat shock protein HSP 90-beta | / | 0.471 | |
| 4gg1 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.471 | |
| 4irn | FAD | AnaB | / | 0.470 | |
| 5dqr | FAD | 7-hydroxymethyl chlorophyll a reductase, chloroplastic | 1.17.7.2 | 0.470 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.468 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.467 | |
| 4mq5 | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.467 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.465 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.465 | |
| 2v1x | ADP | ATP-dependent DNA helicase Q1 | 3.6.4.12 | 0.465 | |
| 2yjx | YJX | Heat shock protein HSP 90-alpha | / | 0.465 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.463 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.463 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.463 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.463 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.463 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.462 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.462 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.462 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.462 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.461 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.460 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.460 | |
| 2yke | YKE | Heat shock protein HSP 90-alpha | / | 0.460 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.460 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.459 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.459 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.459 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.459 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.458 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.457 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.457 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.457 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.457 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.457 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.456 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.456 | |
| 2q5p | 241 | Peroxisome proliferator-activated receptor gamma | / | 0.456 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.455 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.455 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.455 | |
| 1zp3 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.454 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.454 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.454 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.453 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.453 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.453 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.453 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.453 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.453 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.453 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.452 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.452 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.452 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.452 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.452 | |
| 4gyi | ADP | Uncharacterized protein | / | 0.452 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.451 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.451 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.451 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.451 | |
| 3bbt | FMM | Receptor tyrosine-protein kinase erbB-4 | 2.7.10.1 | 0.451 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.451 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.451 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.451 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.450 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.449 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.448 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.448 | |
| 2fwn | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.448 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.448 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.448 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.448 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 1g69 | TZP | Thiamine-phosphate synthase | / | 0.447 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.447 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.447 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.447 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.447 | |
| 2bra | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.446 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.446 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.446 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.446 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.446 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.445 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.445 | |
| 1zdw | FLV | Prenyltransferase | / | 0.445 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 4a33 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.445 | |
| 1dfo | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.444 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.444 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.444 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.444 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.444 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.444 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.443 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.443 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.443 | |
| 3w78 | CBD | FMN-dependent NADH-azoreductase | / | 0.443 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.443 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.442 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.442 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.442 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.442 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.442 | |
| 3mnr | SD1 | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.442 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.442 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.442 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.442 | |
| 5dgt | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.441 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.440 | |
| 3fst | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.440 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.440 | |
| 4n9i | PCG | Catabolite expression activator | / | 0.440 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.440 |