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 |
|---|---|---|---|
| 4h2d | FMN | NADPH-dependent diflavin oxidoreductase 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4h2d | FMN | NADPH-dependent diflavin oxidoreductase 1 | / | 1.000 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.572 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.554 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.554 | |
| 1ja1 | FMN | NADPH--cytochrome P450 reductase | / | 0.553 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.542 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.536 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.509 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.502 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.495 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.492 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.492 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.491 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.489 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.486 | |
| 1ykg | FMN | Sulfite reductase [NADPH] flavoprotein alpha-component | / | 0.485 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.483 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.483 | |
| 4e2x | TYD | Methyltransferase | / | 0.482 | |
| 1yob | FMN | Flavodoxin 2 | / | 0.479 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.475 | |
| 1fue | FMN | Flavodoxin | / | 0.473 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.473 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.473 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.473 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.470 | |
| 5f8f | SFG | Possible transcriptional regulatory protein | / | 0.468 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.467 | |
| 2g9r | G27 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.466 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.466 | |
| 2bsx | NOS | Purine nucleoside phosphorylase | / | 0.464 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.464 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.463 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.463 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.462 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.461 | |
| 1gsn | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.461 | |
| 1j9z | FMN | NADPH--cytochrome P450 reductase | / | 0.461 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.461 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.460 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.460 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.460 | |
| 3s7d | LEU_SER_LYS_LYS_MLZ | N-lysine methyltransferase SMYD2 | / | 0.460 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.460 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.459 | |
| 2rgj | FAD | Flavin-containing monooxygenase | / | 0.459 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.459 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.459 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.459 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.459 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.458 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.458 | |
| 1akr | FMN | Flavodoxin | / | 0.457 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.457 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.457 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.457 | |
| 2fjb | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.457 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.457 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 1dr5 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.456 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.456 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.456 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.456 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.455 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.455 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.455 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.454 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.454 | |
| 3rj0 | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.454 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.454 | |
| 4e2z | JHZ | Methyltransferase | / | 0.454 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.454 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1c7o | PPG | Hemolysin | / | 0.453 | |
| 2an9 | GDP | Guanylate kinase | 2.7.4.8 | 0.453 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.453 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.453 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.453 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.453 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.452 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.452 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.452 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.452 | |
| 2yd0 | BES | Endoplasmic reticulum aminopeptidase 1 | 3.4.11 | 0.452 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.452 | |
| 3m4p | 4AD | Asparaginyl-tRNA synthetase, putative | / | 0.452 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.452 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.452 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.452 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.452 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.451 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.451 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.451 | |
| 2v2q | NVG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.451 | |
| 2z3n | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.451 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.451 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.451 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.450 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.450 | |
| 3zhz | FM7 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.450 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.449 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.449 | |
| 2qtc | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.449 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.449 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4e32 | DWN | Methyltransferase | / | 0.449 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.449 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.449 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.449 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.448 | |
| 1c7f | FMN | Flavodoxin | / | 0.448 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1gra | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.448 | |
| 1zxn | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.448 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.448 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.447 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.447 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.447 | |
| 1lpf | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.447 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.447 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.447 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.447 | |
| 3bj8 | COA | Diamine acetyltransferase 1 | / | 0.447 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.447 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.447 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.447 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.447 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1sui | FRE | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.446 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.446 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.446 | |
| 3h59 | H59 | Genome polyprotein | 2.7.7.48 | 0.446 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.446 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.445 | |
| 3eku | CY9 | Actin-5C | / | 0.445 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.445 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.445 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.445 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.444 | |
| 1n95 | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.444 | |
| 1n95 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1ofv | FMN | Flavodoxin | / | 0.444 | |
| 2cwf | NDP | Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase | / | 0.444 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.444 | |
| 3cow | 52H | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.444 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.444 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.444 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.444 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.443 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.443 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.443 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.443 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.443 | |
| 2qs4 | LY5 | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.443 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.443 | |
| 3tkl | GTP | Ras-related protein Rab-1A | / | 0.443 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.443 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.443 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.443 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.443 | |
| 4xul | GTP | Uncharacterized protein mg662 | / | 0.443 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2r8p | T6F | Transketolase 1 | / | 0.442 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.442 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.442 | |
| 1e2n | RCA | Thymidine kinase | / | 0.441 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.441 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2ylt | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3ndj | JHZ | Methyltransferase | / | 0.441 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.441 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.441 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.441 | |
| 4da8 | BG2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.441 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.441 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.441 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.440 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.440 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.440 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.440 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 3f6s | FMN | Flavodoxin | / | 0.440 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.440 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.440 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4l6s | 1WQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 |