sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4cef | D0T | Integrase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4cef | D0T | Integrase | / | 1.000 | |
| 4cgj | NZL | Integrase | / | 0.703 | |
| 4cea | ZSW | Integrase | / | 0.670 | |
| 4cjp | 4D2 | Integrase | / | 0.664 | |
| 3zsw | ZSW | Integrase | / | 0.663 | |
| 4cjq | VXO | Integrase | / | 0.663 | |
| 4ceq | QCH | Integrase | / | 0.658 | |
| 4cjf | RVN | Integrase | / | 0.651 | |
| 4cf0 | O5U | Integrase | / | 0.638 | |
| 4cf2 | 3GM | Integrase | / | 0.629 | |
| 4cig | X0P | Integrase | / | 0.622 | |
| 3zsx | N44 | Integrase | / | 0.620 | |
| 4ces | NFW | Integrase | / | 0.615 | |
| 3zt2 | ZT2 | Integrase | / | 0.614 | |
| 3zsv | ZSV | Integrase | / | 0.611 | |
| 4ceb | ZSV | Integrase | / | 0.611 | |
| 3zsr | O3N | Integrase | / | 0.604 | |
| 4cez | O3N | Integrase | / | 0.604 | |
| 3zcm | PX3 | Integrase | / | 0.602 | |
| 4ced | 9NS | Integrase | / | 0.600 | |
| 4cec | 2SS | Integrase | / | 0.599 | |
| 4cfb | OM3 | Integrase | / | 0.599 | |
| 4cfc | 7NV | Integrase | / | 0.599 | |
| 4cjk | H39 | Integrase | / | 0.599 | |
| 4cgg | K5Q | Integrase | / | 0.598 | |
| 4ck2 | NVU | Integrase | / | 0.598 | |
| 4cgd | 8P3 | Integrase | / | 0.597 | |
| 4ce9 | O3N | Integrase | / | 0.596 | |
| 4cf8 | V7H | Integrase | / | 0.595 | |
| 4cer | VL4 | Integrase | / | 0.589 | |
| 4cfd | S8Y | Integrase | / | 0.589 | |
| 4cju | JNS | Integrase | / | 0.589 | |
| 3zt0 | ZT0 | Integrase | / | 0.586 | |
| 4cgi | NZL | Integrase | / | 0.586 | |
| 4cj3 | E4F | Integrase | / | 0.585 | |
| 4cj4 | S3G | Integrase | / | 0.583 | |
| 4ck1 | OM1 | Integrase | / | 0.582 | |
| 3zsq | O4N | Integrase | / | 0.579 | |
| 4chy | C5Q | Integrase | / | 0.576 | |
| 4cfa | WOP | Integrase | / | 0.572 | |
| 3zsy | OM3 | Integrase | / | 0.568 | |
| 4cif | JDX | Integrase | / | 0.564 | |
| 4ceo | G0T | Integrase | / | 0.563 | |
| 4cie | Y7N | Integrase | / | 0.559 | |
| 4cj5 | 4VW | Integrase | / | 0.558 | |
| 3zsz | OM2 | Integrase | / | 0.557 | |
| 4cee | B0T | Integrase | / | 0.557 | |
| 4cjs | L0Y | Integrase | / | 0.555 | |
| 4cjr | FYM | Integrase | / | 0.553 | |
| 3zt3 | ZT4 | Integrase | / | 0.548 | |
| 4ck3 | K1T | Integrase | / | 0.545 | |
| 4cf1 | IY7 | Integrase | / | 0.543 | |
| 4cgh | LOZ | Integrase | / | 0.543 | |
| 4cje | Q31 | Integrase | / | 0.539 | |
| 3zt1 | OM1 | Integrase | / | 0.529 | |
| 4chq | CWU | Integrase | / | 0.527 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.477 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.477 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.477 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.472 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.470 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.468 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.465 | |
| 1bdl | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.462 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.462 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.461 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.460 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.458 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.457 | |
| 3pj8 | 404 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.457 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.457 | |
| 5dp2 | NAP | CurF | / | 0.457 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.456 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.456 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.456 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.455 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.455 | |
| 2p3b | 3TL | V-1 protease | / | 0.455 | |
| 3s79 | ASD | Aromatase | 1.14.14.14 | 0.455 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.455 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.455 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.453 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.453 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.453 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.453 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.453 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.453 | |
| 1kqg | MGD | Formate dehydrogenase, nitrate-inducible, major subunit | 1.1.5.6 | 0.452 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.452 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.452 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.452 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.452 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.452 | |
| 3zw3 | ZW3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4cgf | UJ6 | Integrase | / | 0.452 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.452 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.451 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.451 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1ra3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.450 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.450 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.450 | |
| 4nvk | 2NY | Peroxidase | / | 0.450 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.449 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.449 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.449 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.449 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.448 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.448 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.448 | |
| 4ct1 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 4e2d | FMN | Dehydrogenase | / | 0.448 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2bjh | FER | Feruloyl esterase A | 3.1.1.73 | 0.447 | |
| 2brb | PFQ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.447 | |
| 4lb2 | DM5 | Serum albumin | / | 0.447 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.447 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.447 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.446 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.446 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.446 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.446 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.446 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.446 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.446 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.446 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1msn | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.445 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.445 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.445 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.445 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.445 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.445 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 2nmx | M25 | Carbonic anhydrase 1 | 4.2.1.1 | 0.444 | |
| 2pvy | ACP | Fibroblast growth factor receptor 2 | / | 0.444 | |
| 3cs8 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 3qrm | NK7 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.444 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.444 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.444 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 1aj8 | COA | Citrate synthase | / | 0.443 | |
| 1d4k | PI8 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.443 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.443 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.443 | |
| 2xrw | ANP | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.443 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.443 | |
| 3duf | R1T | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.443 | |
| 3hrc | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.443 | |
| 4jin | 1L7 | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.443 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.442 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.442 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.442 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.442 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.442 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.442 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.442 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.441 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1ef9 | 2CP | Methylmalonyl-CoA decarboxylase | 4.1.1.41 | 0.441 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.441 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 3daf | FEG | 5,10-methenyltetrahydromethanopterin hydrogenase | 1.12.98.2 | 0.441 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 4a4q | UX9 | Pol protein | / | 0.441 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.441 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.441 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.441 | |
| 1u4o | NDD | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 2xvu | 9DN | Serum albumin | / | 0.440 | |
| 3dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3edj | BCD | Cyclomaltodextrinase | / | 0.440 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.440 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.440 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.440 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.440 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.440 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 |