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 |
|---|---|---|---|
| 4ymv | ATP | ABC-type polar amino acid transport system, ATPase component |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4ymv | ATP | ABC-type polar amino acid transport system, ATPase component | / | 1.000 | |
| 3ivx | FG6 | Pantothenate synthetase | 6.3.2.1 | 0.505 | |
| 4ymu | ATP | ABC-type polar amino acid transport system, ATPase component | / | 0.504 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.495 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.488 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.484 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.478 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.476 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.476 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.475 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.475 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.475 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.475 | |
| 1ty8 | ADP | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.469 | |
| 3c41 | ANP | Amino acid ABC transporter | / | 0.468 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.467 | |
| 3iaa | TYD | CalG2 | / | 0.467 | |
| 1c7o | PPG | Hemolysin | / | 0.466 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.466 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.466 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.466 | |
| 1f06 | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.465 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.465 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.465 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 2v00 | V15 | Endothiapepsin | 3.4.23.22 | 0.464 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.463 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.463 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.463 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.463 | |
| 4lnb | ED5 | CaaX farnesyltransferase beta subunit Ram1 | / | 0.463 | |
| 1zpt | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.462 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.462 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.462 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.461 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.461 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.460 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.460 | |
| 3eld | SFG | Methyltransferase | / | 0.460 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.460 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.459 | |
| 2c1z | U2F | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.459 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.459 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.459 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.458 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.458 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.458 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.458 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.458 | |
| 4y45 | F91 | Endothiapepsin | 3.4.23.22 | 0.458 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.457 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.457 | |
| 3fst | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.457 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.457 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.456 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.455 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.455 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.454 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.453 | |
| 1zdf | UPG | Glycogenin-1 | 2.4.1.186 | 0.453 | |
| 1zdg | UPG | Glycogenin-1 | 2.4.1.186 | 0.453 | |
| 3b7d | CNI | Glutamate receptor 2 | / | 0.453 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.453 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.453 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.453 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.453 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.453 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.452 | |
| 2prb | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.452 | |
| 4f6r | GDP | Tubulin beta chain | / | 0.452 | |
| 3pmy | 41L | Endothiapepsin | 3.4.23.22 | 0.451 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.451 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.451 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.450 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.450 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.450 | |
| 2fut | H1S | Heparin and heparin-sulfate lyase | / | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.450 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.450 | |
| 4u03 | GTP | Cyclic GMP-AMP synthase | / | 0.450 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.449 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.449 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.448 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.448 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.448 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.448 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.448 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 4de2 | DN3 | Beta-lactamase | / | 0.448 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.448 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.448 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.448 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.447 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.447 | |
| 3fx6 | BPX | Carboxypeptidase A1 | 3.4.17.1 | 0.447 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.447 | |
| 3w8r | ACP | Uridine kinase | / | 0.447 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.447 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.446 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.446 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.446 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.446 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.446 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.445 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.445 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.445 | |
| 3c8b | ARG_ARG_GLY_ILE_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.445 | |
| 3ely | SAH | Methyltransferase | / | 0.445 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3t64 | DU3 | Deoxyuridine 5'-triphosphate nucleotidohydrolase | / | 0.445 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.445 | |
| 4ntc | FAD | Thioredoxin reductase gliT | / | 0.445 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.445 | |
| 1j36 | LPR | Angiotensin-converting enzyme | 3.4.15.1 | 0.444 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.444 | |
| 3hii | PNT | Amiloride-sensitive amine oxidase [copper-containing] | / | 0.444 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3o0o | 5AD | Vitamin B12-dependent ribonucleotide reductase | / | 0.443 | |
| 3pmu | F7L | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.442 | |
| 1ppl | 1Z7 | Penicillopepsin-1 | 3.4.23.20 | 0.442 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.442 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.442 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.442 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.442 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.442 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.442 | |
| 5b0o | ADP | Flagellum-specific ATP synthase | 3.6.3.14 | 0.442 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.441 | |
| 1e80 | 0GQ | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.441 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.441 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.441 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3mk6 | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.441 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.441 | |
| 3ua8 | 08W | Glutamate receptor 2 | / | 0.441 | |
| 4dtb | GMP | APH(2'')-Id | / | 0.441 | |
| 4ei7 | GDP | Plasmid replication protein RepX | / | 0.441 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2d4v | NAD | Isocitrate dehydrogenase [NADP] | / | 0.440 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.440 | |
| 2yvg | NAD | Ferredoxin reductase | / | 0.440 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.440 | |
| 4kgk | GTP | Uncharacterized protein | / | 0.440 | |
| 5c77 | SAH | Protein arginine N-methyltransferase SFM1 | / | 0.440 |