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 |
|---|---|---|---|
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 1.000 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.625 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.606 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.519 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.493 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.493 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.485 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.482 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.480 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.477 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.474 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.474 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.472 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.471 | |
| 1eup | ASD | 6-deoxyerythronolide B hydroxylase | / | 0.471 | |
| 1ha3 | MAU | Elongation factor Tu-A | / | 0.471 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.470 | |
| 4fv3 | EK6 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.468 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.466 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.465 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.464 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.464 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.463 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.463 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.463 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.462 | |
| 3gob | HXX | DdmC | / | 0.460 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.459 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.459 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.458 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.458 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 3vso | EK1 | Peroxisome proliferator-activated receptor gamma | / | 0.458 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.457 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.457 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.455 | |
| 3mtf | A3F | Activin receptor type-1 | 2.7.11.30 | 0.455 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.454 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.454 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.454 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.454 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.454 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.453 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.453 | |
| 2oj9 | BMI | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.453 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.453 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.453 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.452 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.452 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.452 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 2zja | ACP | ATP-dependent DNA helicase Hel308 | / | 0.451 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.451 | |
| 3nbv | ANP | Ketohexokinase | / | 0.451 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 4fv6 | E57 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.451 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.450 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.450 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.450 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.450 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.450 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.450 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.450 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.449 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.449 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.449 | |
| 4b7x | NAP | Probable oxidoreductase | / | 0.449 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.449 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.449 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.449 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.448 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.448 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.448 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.448 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.447 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.447 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.447 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.447 | |
| 2hy0 | 306 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.446 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.446 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.446 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.445 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.445 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.445 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.445 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.445 | |
| 4ftt | 6HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 4kwh | NAP | Reductase homolog | / | 0.445 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 4qec | NAP | ElxO | / | 0.445 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.445 | |
| 1met | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.444 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.444 | |
| 1u54 | ACP | Activated CDC42 kinase 1 | / | 0.444 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.444 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.444 | |
| 2c3k | ABO | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2pwc | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.444 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.444 | |
| 3l4s | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.444 | |
| 3rlr | 3RR | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.444 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 4fsn | A58 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.444 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.443 | |
| 2bxm | IMN | Serum albumin | / | 0.443 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.443 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3zpt | M8Y | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4h4u | NDP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.443 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.442 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.442 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.442 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.442 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.442 | |
| 3r95 | ACO | MccE protein | / | 0.442 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.442 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.442 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.441 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.441 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.441 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.441 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 2oor | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.441 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.441 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.441 | |
| 3b9l | AZZ | Serum albumin | / | 0.441 | |
| 3cgo | JNO | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.441 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.441 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4bib | IEO | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.441 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.441 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.441 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 2bpw | 1IN | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.440 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.440 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.440 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 5a3c | NAD | SIR2 family protein | / | 0.440 |