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 |
|---|---|---|---|
| 4jk4 | DIU | Serum albumin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4jk4 | DIU | Serum albumin | / | 1.000 | |
| 4l8u | 9AZ | Serum albumin | / | 0.510 | |
| 3lu8 | IQX | Serum albumin | / | 0.498 | |
| 4l9k | EHF | Serum albumin | / | 0.497 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.492 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.489 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.489 | |
| 4q0a | 4OA | Vitamin D3 receptor A | / | 0.488 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.487 | |
| 1kk4 | ACO | Streptogramin A acetyltransferase | 2.3.1 | 0.485 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.484 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.484 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.483 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.483 | |
| 3w0a | DS5 | Vitamin D3 receptor | / | 0.483 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.483 | |
| 1rkg | VD1 | Vitamin D3 receptor | / | 0.482 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.482 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.481 | |
| 4fhi | 0S4 | Vitamin D3 receptor A | / | 0.480 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.479 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.478 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.478 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.477 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.477 | |
| 1rjk | VDZ | Vitamin D3 receptor | / | 0.475 | |
| 3h0s | B38 | Acetyl-CoA carboxylase | / | 0.475 | |
| 3kpz | ZNE | Vitamin D3 receptor | / | 0.475 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.475 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.474 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.472 | |
| 2hb7 | O1C | Vitamin D3 receptor | / | 0.472 | |
| 4g1d | 0VK | Vitamin D3 receptor A | / | 0.472 | |
| 3d5f | L41 | Peroxisome proliferator-activated receptor delta | / | 0.471 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.470 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.470 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.470 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.470 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.469 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.469 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.468 | |
| 1s0z | EB1 | Vitamin D3 receptor | / | 0.467 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.467 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.467 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.467 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.467 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.466 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.465 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.465 | |
| 3two | NDP | Mannitol dehydrogenase | / | 0.465 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.464 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.464 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.463 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.463 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.463 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.463 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.463 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.463 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.463 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.462 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.461 | |
| 5ifi | PRX | Acetyl-coenzyme A synthetase | / | 0.461 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.460 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.460 | |
| 3ute | FAD | UDP-galactopyranose mutase | / | 0.460 | |
| 4nr4 | 2LK | CREB-binding protein | / | 0.460 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.459 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.459 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.459 | |
| 2o4r | VD5 | Vitamin D3 receptor | / | 0.459 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.459 | |
| 4l9q | 9TP | Serum albumin | / | 0.459 | |
| 2has | C3O | Vitamin D3 receptor | / | 0.458 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.458 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.458 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.458 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.458 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.457 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.457 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.457 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.457 | |
| 4o8f | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.456 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.456 | |
| 4b7s | QLE | Cytochrome P450 monooxygenase PikC | / | 0.456 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.456 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.455 | |
| 2cjm | ATP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.455 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.455 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.455 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.455 | |
| 4fdp | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.455 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.455 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.455 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.455 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.454 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.454 | |
| 4fhh | 0U3 | Vitamin D3 receptor A | / | 0.454 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.454 | |
| 2c7x | NRB | Cytochrome P450 monooxygenase PikC | / | 0.453 | |
| 2gtk | 208 | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.453 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.453 | |
| 4hdg | GTP | Genome polyprotein | 2.7.7.48 | 0.453 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.453 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.452 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.452 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.452 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.452 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 4y8v | ADP | Acyl-CoA synthetase (NDP forming) | / | 0.452 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1ngi | ANP | Heat shock cognate 71 kDa protein | / | 0.451 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.451 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.450 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.450 | |
| 4a33 | MYA | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.450 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.450 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.450 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.449 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2e48 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.449 | |
| 2nua | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.449 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.449 | |
| 3eql | MXP | DNA-directed RNA polymerase subunit beta | / | 0.449 | |
| 3eql | MXP | DNA-directed RNA polymerase subunit beta' | / | 0.449 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.449 | |
| 4g2h | 0VQ | Vitamin D3 receptor A | / | 0.449 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.449 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2vxo | XMP | GMP synthase [glutamine-hydrolyzing] | 6.3.5.2 | 0.448 | |
| 2zla | VDB | Vitamin D3 receptor | / | 0.448 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.448 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.448 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.448 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.448 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.448 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.448 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.447 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.447 | |
| 3ttj | JBI | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.447 | |
| 4kzo | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.447 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.446 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.446 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 2y98 | MIV | Mycinamicin IV hydroxylase/epoxidase | / | 0.446 | |
| 2zno | S44 | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 3m7r | VDX | Vitamin D3 receptor | / | 0.446 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.446 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.446 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.446 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.446 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.445 | |
| 2j07 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.445 | |
| 2jfg | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.445 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.445 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta | / | 0.445 | |
| 3dxj | NE6 | DNA-directed RNA polymerase subunit beta' | / | 0.445 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.445 | |
| 4awq | 592 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4ubs | DIF | Pentalenic acid synthase | 1.14.15.11 | 0.445 | |
| 4wa9 | AXI | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.445 | |
| 1nyx | DRF | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 1tw4 | CHD | Fatty acid-binding protein, liver | / | 0.444 | |
| 2cdu | FAD | NADH oxidase | / | 0.444 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2nu9 | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.444 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.444 | |
| 3inm | NDP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.444 | |
| 3v9v | 21L | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.444 | |
| 4b13 | NHW | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.444 | |
| 4xey | 1N1 | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.444 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.444 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.443 | |
| 3lb8 | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.443 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.443 | |
| 4phl | PIL | Phosphodiesterase | / | 0.443 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.443 | |
| 5eox | ADP | Type 4 fimbrial biogenesis protein PilM | / | 0.443 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.442 | |
| 1hwz | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.442 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 1iyz | NDP | Probable quinone oxidoreductase | / | 0.442 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.442 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.442 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3inw | JZB | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3ldo | ANP | 78 kDa glucose-regulated protein | / | 0.442 | |
| 3p99 | LNP | Lanosterol 14-alpha-demethylase | / | 0.442 | |
| 3stw | 2TD | Methylketone synthase I | / | 0.442 | |
| 3zuy | TCH | Transporter | / | 0.442 | |
| 4hee | 14R | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.442 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.442 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2jd0 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.441 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2wpx | ACO | Orf14 | / | 0.441 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.441 | |
| 3stu | DK3 | Methylketone synthase I | / | 0.441 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.441 | |
| 3zux | TCH | Transporter | / | 0.441 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.440 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.440 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.440 | |
| 2hfp | NSI | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.440 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.440 | |
| 4o2b | LOC | Tubulin beta-2B chain | / | 0.440 | |
| 5eg3 | ACP | Fibroblast growth factor receptor 2 | / | 0.440 |