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 |
|---|---|---|---|
| 4cju | JNS | Integrase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4cju | JNS | Integrase | / | 1.000 | |
| 4ceq | QCH | Integrase | / | 0.625 | |
| 4ces | NFW | Integrase | / | 0.623 | |
| 4cf2 | 3GM | Integrase | / | 0.618 | |
| 4ceo | G0T | Integrase | / | 0.607 | |
| 4cfd | S8Y | Integrase | / | 0.604 | |
| 3zsr | O3N | Integrase | / | 0.599 | |
| 4cez | O3N | Integrase | / | 0.599 | |
| 4cjf | RVN | Integrase | / | 0.596 | |
| 4cec | 2SS | Integrase | / | 0.595 | |
| 4cea | ZSW | Integrase | / | 0.594 | |
| 4cf8 | V7H | Integrase | / | 0.588 | |
| 4cfc | 7NV | Integrase | / | 0.588 | |
| 4cgj | NZL | Integrase | / | 0.588 | |
| 4cfa | WOP | Integrase | / | 0.585 | |
| 4cf0 | O5U | Integrase | / | 0.584 | |
| 3zsw | ZSW | Integrase | / | 0.583 | |
| 4cie | Y7N | Integrase | / | 0.581 | |
| 4ced | 9NS | Integrase | / | 0.580 | |
| 4ce9 | O3N | Integrase | / | 0.579 | |
| 4cf1 | IY7 | Integrase | / | 0.579 | |
| 4cef | D0T | Integrase | / | 0.577 | |
| 4cer | VL4 | Integrase | / | 0.577 | |
| 4cgi | NZL | Integrase | / | 0.574 | |
| 3zt0 | ZT0 | Integrase | / | 0.567 | |
| 4cee | B0T | Integrase | / | 0.564 | |
| 4ck2 | NVU | Integrase | / | 0.563 | |
| 4cj3 | E4F | Integrase | / | 0.561 | |
| 4cfb | OM3 | Integrase | / | 0.560 | |
| 4cjk | H39 | Integrase | / | 0.556 | |
| 4cjp | 4D2 | Integrase | / | 0.555 | |
| 4ck3 | K1T | Integrase | / | 0.554 | |
| 3zt3 | ZT4 | Integrase | / | 0.551 | |
| 4cgg | K5Q | Integrase | / | 0.551 | |
| 3zsv | ZSV | Integrase | / | 0.550 | |
| 4ceb | ZSV | Integrase | / | 0.550 | |
| 4chq | CWU | Integrase | / | 0.548 | |
| 4cgd | 8P3 | Integrase | / | 0.543 | |
| 4cif | JDX | Integrase | / | 0.543 | |
| 4cjr | FYM | Integrase | / | 0.539 | |
| 3zsx | N44 | Integrase | / | 0.538 | |
| 3zt2 | ZT2 | Integrase | / | 0.532 | |
| 4cjq | VXO | Integrase | / | 0.532 | |
| 4cgh | LOZ | Integrase | / | 0.530 | |
| 4cjs | L0Y | Integrase | / | 0.530 | |
| 4ck1 | OM1 | Integrase | / | 0.530 | |
| 4cig | X0P | Integrase | / | 0.527 | |
| 3zsq | O4N | Integrase | / | 0.520 | |
| 3zsy | OM3 | Integrase | / | 0.519 | |
| 4cj5 | 4VW | Integrase | / | 0.515 | |
| 4cje | Q31 | Integrase | / | 0.512 | |
| 4chy | C5Q | Integrase | / | 0.510 | |
| 3zcm | PX3 | Integrase | / | 0.509 | |
| 3zsz | OM2 | Integrase | / | 0.509 | |
| 3zt1 | OM1 | Integrase | / | 0.505 | |
| 4cj4 | S3G | Integrase | / | 0.500 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.486 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.485 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.485 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.482 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.470 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.470 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.469 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.468 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.467 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.466 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.465 | |
| 3cgf | JNF | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.464 | |
| 1fml | RTL | Retinol dehydratase | / | 0.463 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.462 | |
| 4aqc | 88A | Tyrosine-protein kinase JAK2 | / | 0.462 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.461 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.461 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.460 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.460 | |
| 3q71 | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.460 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.459 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.459 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.458 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.458 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.458 | |
| 1tsx | UMP | Thymidylate synthase | / | 0.457 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.457 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.457 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.456 | |
| 3nww | 3NW | Mitogen-activated protein kinase 14 | / | 0.456 | |
| 3qd0 | 3Q4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.456 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.456 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.456 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.455 | |
| 5iqi | GNP | Bifunctional AAC/APH | 2.3.1 | 0.455 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.454 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.454 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.454 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.454 | |
| 4loq | SB4 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.454 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.453 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.453 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.453 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.453 | |
| 4fv0 | EK3 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.453 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.453 | |
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.452 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.452 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.452 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.452 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.452 | |
| 3p23 | ADP | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.452 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.451 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.451 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.451 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.450 | |
| 1gqt | ACP | Ribokinase | / | 0.450 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.450 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.450 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.450 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.449 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.449 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.449 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.449 | |
| 1fp2 | HMO | Isoflavone-7-O-methyltransferase 8 | 2.1.1.150 | 0.448 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.448 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.448 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 4cgf | UJ6 | Integrase | / | 0.448 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 4fod | 0UV | ALK tyrosine kinase receptor | 2.7.10.1 | 0.448 | |
| 4kip | 1R9 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 4o70 | 1QK | Bromodomain-containing protein 4 | / | 0.448 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.447 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.447 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3g8e | IS1 | Nicotinamide phosphoribosyltransferase | 2.4.2.12 | 0.447 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.447 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.447 | |
| 4pl4 | ADP | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.447 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.446 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.446 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 2ii5 | CO6 | Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial | 2.3.1.168 | 0.446 | |
| 3stv | 3HO | Methylketone synthase I | / | 0.446 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.446 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.445 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.445 | |
| 1ol6 | ATP | Aurora kinase A | 2.7.11.1 | 0.445 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.445 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.445 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.445 | |
| 2j14 | GNI | Peroxisome proliferator-activated receptor delta | / | 0.445 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.445 | |
| 4em9 | TCE | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.445 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.444 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.444 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.444 | |
| 4pkl | 1GH | Uncharacterized protein | / | 0.444 | |
| 4u7w | NDP | MxaA | / | 0.444 | |
| 2owu | SAH | Diphthine synthase | / | 0.443 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.443 | |
| 4fv6 | E57 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.443 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.443 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.443 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.443 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.443 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.442 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.442 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.442 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.442 | |
| 4jaz | STL | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.442 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.441 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.441 | |
| 2buj | STU | Serine/threonine-protein kinase 16 | / | 0.441 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.441 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.441 | |
| 4bdh | WVI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.441 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.441 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.441 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.440 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.440 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.440 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.440 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.440 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 3t8o | ATP | Rhodopsin kinase | / | 0.440 | |
| 3tuc | FPW | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.440 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.440 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.440 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.440 |