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 |
|---|---|---|---|
| 4ceq | QCH | Integrase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4ceq | QCH | Integrase | / | 1.000 | |
| 4cef | D0T | Integrase | / | 0.636 | |
| 3zsr | O3N | Integrase | / | 0.627 | |
| 4ce9 | O3N | Integrase | / | 0.627 | |
| 4cez | O3N | Integrase | / | 0.627 | |
| 4cec | 2SS | Integrase | / | 0.609 | |
| 4ceo | G0T | Integrase | / | 0.608 | |
| 4cer | VL4 | Integrase | / | 0.595 | |
| 4cf8 | V7H | Integrase | / | 0.595 | |
| 4cea | ZSW | Integrase | / | 0.593 | |
| 4cgd | 8P3 | Integrase | / | 0.593 | |
| 3zt0 | ZT0 | Integrase | / | 0.591 | |
| 4cig | X0P | Integrase | / | 0.587 | |
| 4cf0 | O5U | Integrase | / | 0.583 | |
| 4cgg | K5Q | Integrase | / | 0.579 | |
| 4cju | JNS | Integrase | / | 0.578 | |
| 4cfb | OM3 | Integrase | / | 0.573 | |
| 3zsw | ZSW | Integrase | / | 0.571 | |
| 4cgj | NZL | Integrase | / | 0.569 | |
| 4ced | 9NS | Integrase | / | 0.565 | |
| 4cfa | WOP | Integrase | / | 0.564 | |
| 4cje | Q31 | Integrase | / | 0.564 | |
| 4cee | B0T | Integrase | / | 0.561 | |
| 4ces | NFW | Integrase | / | 0.561 | |
| 4cfc | 7NV | Integrase | / | 0.561 | |
| 3zsv | ZSV | Integrase | / | 0.559 | |
| 4ceb | ZSV | Integrase | / | 0.559 | |
| 4cgi | NZL | Integrase | / | 0.559 | |
| 4cjk | H39 | Integrase | / | 0.557 | |
| 4cf2 | 3GM | Integrase | / | 0.555 | |
| 4cjf | RVN | Integrase | / | 0.555 | |
| 4ck2 | NVU | Integrase | / | 0.555 | |
| 4cjq | VXO | Integrase | / | 0.553 | |
| 4ck1 | OM1 | Integrase | / | 0.547 | |
| 3zsq | O4N | Integrase | / | 0.546 | |
| 4cjr | FYM | Integrase | / | 0.546 | |
| 4cfd | S8Y | Integrase | / | 0.544 | |
| 4cif | JDX | Integrase | / | 0.543 | |
| 4cjp | 4D2 | Integrase | / | 0.543 | |
| 3zsy | OM3 | Integrase | / | 0.539 | |
| 4cj3 | E4F | Integrase | / | 0.537 | |
| 4cie | Y7N | Integrase | / | 0.534 | |
| 3zt1 | OM1 | Integrase | / | 0.533 | |
| 3zt3 | ZT4 | Integrase | / | 0.527 | |
| 4chy | C5Q | Integrase | / | 0.523 | |
| 4ck3 | K1T | Integrase | / | 0.523 | |
| 3zsz | OM2 | Integrase | / | 0.521 | |
| 3zt2 | ZT2 | Integrase | / | 0.521 | |
| 4cf1 | IY7 | Integrase | / | 0.517 | |
| 4cgh | LOZ | Integrase | / | 0.512 | |
| 4cj5 | 4VW | Integrase | / | 0.511 | |
| 4chq | CWU | Integrase | / | 0.510 | |
| 3zsx | N44 | Integrase | / | 0.502 | |
| 4cj4 | S3G | Integrase | / | 0.499 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.493 | |
| 3zcm | PX3 | Integrase | / | 0.493 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.487 | |
| 4cjs | L0Y | Integrase | / | 0.485 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.484 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.476 | |
| 1qvn | FRI | Interleukin-2 | / | 0.472 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.471 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.471 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.468 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.468 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.468 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.468 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.467 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.465 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.465 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.463 | |
| 2bjh | FER | Feruloyl esterase A | 3.1.1.73 | 0.462 | |
| 2xvu | 9DN | Serum albumin | / | 0.462 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.462 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.462 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.462 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.461 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 3r35 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.461 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.461 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.461 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.460 | |
| 1pw6 | FRB | Interleukin-2 | / | 0.460 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.460 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.458 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.458 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.458 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.458 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.457 | |
| 2wuf | KEM | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.457 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.457 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.457 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.457 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.455 | |
| 2wxv | WXV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.455 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.454 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.454 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.453 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.453 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.452 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.452 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.452 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.452 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.452 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.451 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1h74 | AGS | Homoserine kinase | 2.7.1.39 | 0.451 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 5doz | NDP | JamJ | / | 0.451 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.450 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 3ggf | GVD | Serine/threonine-protein kinase 26 | / | 0.450 | |
| 4hnh | NAP | NAD-dependent epimerase/dehydratase | / | 0.450 | |
| 5dp2 | NAP | CurF | / | 0.450 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.449 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.449 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.449 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 2y3r | TRK | TamL | / | 0.448 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.448 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.448 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.447 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.447 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.446 | |
| 2cib | CM6 | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.446 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.446 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.446 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.446 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.446 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.446 | |
| 4k9d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.446 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.445 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.445 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.445 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.445 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.445 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.445 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 4bzn | UGX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.445 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.445 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.445 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.445 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1msn | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3ac3 | KSH | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.444 | |
| 3d3e | D3E | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.444 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.444 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.444 | |
| 4xuh | SFI | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.444 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.443 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.443 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.443 | |
| 1ppj | ANY | Cytochrome b | / | 0.443 | |
| 1u4o | NDD | L-lactate dehydrogenase | 1.1.1.27 | 0.443 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.443 | |
| 2ohv | NHL | Glutamate racemase | / | 0.443 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.443 | |
| 3qu0 | X40 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3wle | NAD | (R)-specific carbonyl reductase | / | 0.443 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.443 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.443 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.442 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.442 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.442 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.442 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.442 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.442 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.442 | |
| 2xs0 | ANP | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.442 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.442 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.442 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.441 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.441 | |
| 3b8r | 887 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.441 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3vs3 | VSE | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.441 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.441 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.440 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.440 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.440 | |
| 2bal | PQA | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.440 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 3cs8 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3e5r | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.440 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.440 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.440 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.440 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.440 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 |