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 |
|---|---|---|---|
| 4ceq | QCH | Integrase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity 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 | |
| 3zt0 | ZT0 | Integrase | / | 0.592 | |
| 4cgd | 8P3 | Integrase | / | 0.592 | |
| 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 | |
| 4ck2 | NVU | Integrase | / | 0.571 | |
| 4cgj | NZL | Integrase | / | 0.568 | |
| 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 | |
| 4cjq | VXO | Integrase | / | 0.553 | |
| 4cfd | S8Y | Integrase | / | 0.549 | |
| 4ck1 | OM1 | Integrase | / | 0.547 | |
| 3zsq | O4N | Integrase | / | 0.546 | |
| 4cjr | FYM | Integrase | / | 0.546 | |
| 4cif | JDX | Integrase | / | 0.545 | |
| 4cjp | 4D2 | Integrase | / | 0.543 | |
| 3zsz | OM2 | Integrase | / | 0.542 | |
| 3zsy | OM3 | Integrase | / | 0.539 | |
| 4chy | C5Q | Integrase | / | 0.538 | |
| 4cj3 | E4F | Integrase | / | 0.537 | |
| 4cie | Y7N | Integrase | / | 0.534 | |
| 3zt1 | OM1 | Integrase | / | 0.533 | |
| 3zt3 | ZT4 | Integrase | / | 0.527 | |
| 4ck3 | K1T | Integrase | / | 0.523 | |
| 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 | |
| 3zcm | PX3 | Integrase | / | 0.493 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.486 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.485 | |
| 4cjs | L0Y | Integrase | / | 0.485 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.477 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.472 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.469 | |
| 2nmx | M25 | Carbonic anhydrase 1 | 4.2.1.1 | 0.469 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.469 | |
| 1qvn | FRI | Interleukin-2 | / | 0.468 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.465 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.464 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.463 | |
| 1pw6 | FRB | Interleukin-2 | / | 0.462 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.462 | |
| 2bjh | FER | Feruloyl esterase A | 3.1.1.73 | 0.461 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.461 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.461 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.460 | |
| 2o7p | NAP | Riboflavin biosynthesis protein RibD | / | 0.460 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.459 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.458 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.458 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.457 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.457 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 3c0i | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.456 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.456 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.456 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.455 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.455 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.455 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1h74 | AGS | Homoserine kinase | 2.7.1.39 | 0.454 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.454 | |
| 2wxv | WXV | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 3r35 | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.453 | |
| 4l4x | NDP | AmphI | / | 0.453 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.452 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.452 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.452 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.452 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.452 | |
| 1pow | FAD | Pyruvate oxidase | 1.2.3.3 | 0.451 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.451 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.450 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.450 | |
| 4e2d | FMN | Dehydrogenase | / | 0.450 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.450 | |
| 4hnh | NAP | NAD-dependent epimerase/dehydratase | / | 0.450 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.450 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.449 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.448 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.448 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.448 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.447 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.447 | |
| 3ggf | GVD | Serine/threonine-protein kinase 26 | / | 0.447 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.447 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.447 | |
| 5dp2 | NAP | CurF | / | 0.447 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.446 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.446 | |
| 1dkf | BMS | Retinoic acid receptor alpha | / | 0.445 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.445 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.445 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.445 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.445 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.444 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.444 | |
| 3ac3 | KSH | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.444 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.444 | |
| 4bdh | WVI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.444 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.444 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.443 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.443 | |
| 2ohv | NHL | Glutamate racemase | / | 0.443 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.443 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.443 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.443 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.443 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2bal | PQA | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 2xs0 | ANP | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.442 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.442 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 3mg3 | ECH | Orange carotenoid-binding protein | / | 0.442 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.441 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.441 | |
| 1u4o | NDD | L-lactate dehydrogenase | 1.1.1.27 | 0.441 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3b8r | 887 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.441 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 4bzn | UGX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.441 | |
| 5doz | NDP | JamJ | / | 0.441 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.440 | |
| 3gu8 | 3GU | Death-associated protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.440 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4lva | 20M | Nicotinamide phosphoribosyltransferase | 2.4.2.12 | 0.440 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.440 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.440 |