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 |
|---|---|---|---|
| 4cef | D0T | Integrase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site 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 | |
| 4ce9 | O3N | Integrase | / | 0.596 | |
| 4cf8 | V7H | Integrase | / | 0.595 | |
| 4cgd | 8P3 | Integrase | / | 0.591 | |
| 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 | |
| 4ck2 | NVU | Integrase | / | 0.583 | |
| 4ck1 | OM1 | Integrase | / | 0.582 | |
| 3zsq | O4N | Integrase | / | 0.579 | |
| 4cfa | WOP | Integrase | / | 0.574 | |
| 3zsy | OM3 | Integrase | / | 0.568 | |
| 4cif | JDX | Integrase | / | 0.564 | |
| 4ceo | G0T | Integrase | / | 0.563 | |
| 4chy | C5Q | Integrase | / | 0.560 | |
| 4cie | Y7N | Integrase | / | 0.559 | |
| 4cj5 | 4VW | Integrase | / | 0.558 | |
| 4cee | B0T | Integrase | / | 0.557 | |
| 4cjs | L0Y | Integrase | / | 0.555 | |
| 4cjr | FYM | Integrase | / | 0.553 | |
| 3zt3 | ZT4 | Integrase | / | 0.548 | |
| 3zsz | OM2 | Integrase | / | 0.545 | |
| 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 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.480 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.478 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.477 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.476 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.469 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.468 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.467 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.466 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.466 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.465 | |
| 3cs8 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.464 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.463 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.463 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.462 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.461 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.461 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.461 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 5dp2 | NAP | CurF | / | 0.461 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.461 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.460 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.459 | |
| 4wdg | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.459 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.458 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.457 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.457 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.457 | |
| 2p3b | 3TL | V-1 protease | / | 0.457 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.457 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.457 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.457 | |
| 4kgm | ATP | Uncharacterized protein | / | 0.457 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.456 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.456 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.456 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.456 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.456 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.456 | |
| 3pj8 | 404 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.455 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.455 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.455 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.454 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.454 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4jaz | STL | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.453 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.453 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.453 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.453 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.453 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.453 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1kqg | MGD | Formate dehydrogenase, nitrate-inducible, major subunit | 1.1.5.6 | 0.452 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4cgf | UJ6 | Integrase | / | 0.452 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.452 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.452 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.451 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.451 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.451 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.451 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.451 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.450 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.450 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.450 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.449 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.449 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.449 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.449 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.449 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.449 | |
| 4iac | ACP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 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 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.448 | |
| 1ef9 | 2CP | Methylmalonyl-CoA decarboxylase | 4.1.1.41 | 0.448 | |
| 2bjh | FER | Feruloyl esterase A | 3.1.1.73 | 0.448 | |
| 2xrw | ANP | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.448 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 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 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.447 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.447 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.447 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.447 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.447 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.447 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.446 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.446 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 2pvy | ACP | Fibroblast growth factor receptor 2 | / | 0.446 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.446 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 1msn | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2b4r | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.445 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.445 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.445 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.445 | |
| 2xvu | 9DN | Serum albumin | / | 0.445 | |
| 3dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.445 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.445 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.445 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 2am2 | 2LG | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.444 | |
| 2r43 | G3G | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.444 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.444 | |
| 4a4q | UX9 | Pol protein | / | 0.444 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4fv7 | E94 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.444 | |
| 1d4k | PI8 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1fm9 | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.443 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.443 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.443 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.443 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.443 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.443 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.443 | |
| 4tzk | 641 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.442 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.442 | |
| 2xvw | 9NR | Serum albumin | / | 0.442 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3gob | HXX | DdmC | / | 0.442 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.442 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.442 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.442 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3pe2 | E1B | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.442 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1ec2 | BEJ | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.441 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 2wxv | WXV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 3c16 | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 3c16 | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.441 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.440 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.440 | |
| 3hrc | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.440 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.440 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.440 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.440 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.440 | |
| 4u03 | GTP | Cyclic GMP-AMP synthase | / | 0.440 |