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 |
|---|---|---|---|
| 2fhn | BNI | Avidin-related protein 4/5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2fhn | BNI | Avidin-related protein 4/5 | / | 1.000 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.568 | |
| 1mk5 | BTN | Streptavidin | / | 0.529 | |
| 2avi | BTN | Avidin | / | 0.526 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.523 | |
| 2uyw | BTN | Avd protein | / | 0.516 | |
| 2izh | BTN | Streptavidin | / | 0.512 | |
| 4bx7 | B4F | Streptavidin | / | 0.512 | |
| 2rtf | BTN | Streptavidin | / | 0.501 | |
| 1avd | BTN | Avidin | / | 0.500 | |
| 4dne | DTB | Streptavidin | / | 0.500 | |
| 2uz2 | BTN | Avd protein | / | 0.499 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.496 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.494 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.491 | |
| 2rtg | BTN | Streptavidin | / | 0.490 | |
| 3ry2 | BTN | Streptavidin | / | 0.490 | |
| 2rto | IMI | Streptavidin | / | 0.489 | |
| 1stp | BTN | Streptavidin | / | 0.488 | |
| 2izf | BTN | Streptavidin | / | 0.485 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.484 | |
| 2izl | IMI | Streptavidin | / | 0.484 | |
| 2izg | BTN | Streptavidin | / | 0.483 | |
| 2rtq | IMI | Streptavidin | / | 0.482 | |
| 3wyq | BTN | Streptavidin | / | 0.480 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.478 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.478 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.477 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.477 | |
| 1srg | MHB | Streptavidin | / | 0.477 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.476 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.475 | |
| 1df8 | BTN | Streptavidin | / | 0.474 | |
| 3wzn | BTN | Streptavidin | / | 0.474 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.471 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.471 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.471 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.469 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.468 | |
| 1sri | DMB | Streptavidin | / | 0.467 | |
| 1swp | BTQ | Streptavidin | / | 0.467 | |
| 1sre | HAB | Streptavidin | / | 0.466 | |
| 3vfq | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.466 | |
| 4bj8 | BTN | Avidin | / | 0.466 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.465 | |
| 2rtr | IMI | Streptavidin | / | 0.465 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.464 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.464 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.464 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.464 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.463 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.463 | |
| 2rtn | IMI | Streptavidin | / | 0.463 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 1srf | MTB | Streptavidin | / | 0.462 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.461 | |
| 2c4i | BTN | Avidin | / | 0.461 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.461 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.461 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.461 | |
| 4z28 | BTN | Hoefavidin | / | 0.461 | |
| 4d86 | ADP | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.460 | |
| 4gda | BTN | Streptavidin | / | 0.460 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.460 | |
| 1swt | BTN | Streptavidin | / | 0.459 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.459 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.459 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.459 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.459 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.458 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.458 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.457 | |
| 1swn | BTN | Streptavidin | / | 0.457 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.457 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.457 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.457 | |
| 2y3f | BTN | Streptavidin | / | 0.456 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.456 | |
| 4irn | FAD | AnaB | / | 0.456 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.455 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.455 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.455 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.454 | |
| 1swe | BTN | Streptavidin | / | 0.454 | |
| 2bfr | ADP | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.454 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.454 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.454 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1ppj | ANY | Cytochrome b | / | 0.453 | |
| 1rxh | BNI | Streptavidin | / | 0.453 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.453 | |
| 4die | C5P | Cytidylate kinase | / | 0.453 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.453 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.452 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.452 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.452 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.452 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.452 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.452 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.452 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.452 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.452 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.452 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.452 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.452 | |
| 1vza | UMP | Thymidylate synthase | / | 0.451 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.451 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.451 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 1luq | BTN | Streptavidin | / | 0.450 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.450 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.450 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.450 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.450 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.450 | |
| 5a3b | APR | SIR2 family protein | / | 0.450 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.450 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.449 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.449 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.449 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.449 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.449 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.449 | |
| 2rtd | BTN | Streptavidin | / | 0.449 | |
| 4kqq | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.449 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.448 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.448 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.448 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4g6h | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.448 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.448 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.447 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 2vht | ATP | NTPase P4 | / | 0.447 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.447 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.447 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3t8w | DGZ | M17 leucyl aminopeptidase | / | 0.447 | |
| 4e2b | FMN | Dehydrogenase | / | 0.447 | |
| 1i9h | BNI | Streptavidin | / | 0.446 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.446 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.446 | |
| 2rtm | IMI | Streptavidin | / | 0.446 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.446 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.446 | |
| 4wri | OKA | Okadaic acid binding protein 2-alpha | / | 0.446 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.446 | |
| 5dp2 | NAP | CurF | / | 0.446 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.445 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.445 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.445 | |
| 3vgw | NVZ | Avidin | / | 0.445 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.445 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.445 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.444 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.444 | |
| 2rte | BTN | Streptavidin | / | 0.444 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.444 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.444 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.444 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.444 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.444 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.444 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.443 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.443 | |
| 2qjo | NAD | Bifunctional NMN adenylyltransferase/Nudix hydrolase | 2.7.7.1 | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.443 | |
| 4l4x | NDP | AmphI | / | 0.443 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.442 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.442 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.442 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.442 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.442 | |
| 5kwv | ANP | Pantothenate synthetase | / | 0.442 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.441 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.441 | |
| 1lcw | SHM | Streptavidin | / | 0.441 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.441 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.441 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.441 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.441 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.441 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.441 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.440 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.440 | |
| 1srj | NAB | Streptavidin | / | 0.440 | |
| 1swp | BTN | Streptavidin | / | 0.440 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.440 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.440 | |
| 2rtp | IMI | Streptavidin | / | 0.440 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.440 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.440 | |
| 3up3 | XCA | aceDAF-12 | / | 0.440 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.440 |