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 |
|---|---|---|---|
| 3r3s | NAD | Putative oxidoreductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3r3s | NAD | Putative oxidoreductase | / | 1.000 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.625 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.562 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.560 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.558 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.557 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.549 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.546 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.544 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.544 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.541 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.540 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.529 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.528 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.528 | |
| 1iy8 | NAD | Levodione reductase | / | 0.527 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.527 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.526 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.526 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.526 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.524 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.524 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.523 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.523 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.522 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.522 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.521 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.521 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.521 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.521 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.520 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.519 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.518 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.517 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.517 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.517 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.516 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.516 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.516 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.515 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.515 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.515 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.514 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.514 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.513 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.513 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.511 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.508 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.507 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.506 | |
| 3sju | NDP | Keto reductase | / | 0.506 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.506 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.506 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.505 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.505 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.504 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.502 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.502 | |
| 1sny | NAP | LD36273p | / | 0.501 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.501 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.500 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.500 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.500 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.499 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.498 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.498 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.498 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.497 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.497 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.496 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.494 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.491 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.489 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.489 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.488 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.488 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.488 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.487 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.486 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.486 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.486 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.486 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.485 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.485 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.485 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.484 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.484 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.484 | |
| 4wlo | NAI | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.484 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.483 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.482 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.481 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.480 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.480 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.480 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.479 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.479 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.479 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.479 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.477 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.475 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.475 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.475 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.475 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.474 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.474 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.474 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.473 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.473 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.473 | |
| 1mgo | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.472 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.472 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.472 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.472 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.471 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.470 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.469 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.467 | |
| 4qed | NAP | ElxO | / | 0.467 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.466 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.466 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.465 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.465 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.465 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.465 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.465 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.465 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.464 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.463 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.463 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.463 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.463 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.463 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.463 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.463 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.462 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.461 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.460 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.459 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.459 | |
| 3ieu | GDP | GTPase Era | / | 0.459 | |
| 3uce | NDP | Dehydrogenase | / | 0.459 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.458 | |
| 2z1m | NDP | GDP-mannose 4,6-dehydratase | / | 0.458 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.457 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.457 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.457 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.455 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.454 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.454 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.454 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.454 | |
| 4tlx | FDA | KtzI | / | 0.454 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.453 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.453 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.452 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.452 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.452 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.452 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.452 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.452 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.451 | |
| 4qec | NAP | ElxO | / | 0.451 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.450 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.449 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.449 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.448 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.448 | |
| 1b3r | NAD | Adenosylhomocysteinase | 3.3.1.1 | 0.447 | |
| 3bmo | NAP | Pteridine reductase | / | 0.447 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.447 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.445 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.445 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.444 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.443 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.442 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.442 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.442 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.442 | |
| 4j4b | NAI | Uncharacterized protein | / | 0.442 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.441 | |
| 1uay | ADN | Oxidoreductase | / | 0.440 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.440 |