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 |
|---|---|---|---|
| 4nmc | FAD | Bifunctional protein PutA |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4nmc | FAD | Bifunctional protein PutA | / | 1.000 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.489 | |
| 4l4x | NDP | AmphI | / | 0.481 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.480 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.477 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.475 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.472 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.471 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.470 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.469 | |
| 2bun | FAD | AppA protein | / | 0.468 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.467 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.467 | |
| 2qn3 | F55 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.467 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.467 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.466 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.465 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.465 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.465 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.465 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.465 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.464 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.464 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.464 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.463 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.463 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.463 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.462 | |
| 3rbq | GLY_ALA_GLY_ALA_DAO | Protein unc-119 homolog A | / | 0.461 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4die | C5P | Cytidylate kinase | / | 0.460 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 4gu6 | 10N | Focal adhesion kinase 1 | 2.7.10.2 | 0.460 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.459 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.459 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.459 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.459 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.457 | |
| 1m9m | 6NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.457 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.457 | |
| 3n8n | N88 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.457 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 1r8c | UTP | CCA-adding enzyme | 2.7.7.72 | 0.456 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.456 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.456 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 4v12 | POG | MaoC like domain protein | / | 0.456 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.455 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.454 | |
| 1gqt | ACP | Ribokinase | / | 0.454 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2w6n | OA2 | Biotin carboxylase | 6.3.4.14 | 0.454 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.454 | |
| 3mvm | 39P | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.453 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.452 | |
| 2cdu | FAD | NADH oxidase | / | 0.452 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.452 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 3hz5 | Z64 | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.452 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.452 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.452 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.452 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.451 | |
| 2cgx | 3D3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.451 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.451 | |
| 3rga | ILD | Epoxide hydrolase LasB | 5.5.1 | 0.451 | |
| 3rwp | ABQ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.451 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.451 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1equ | EQI | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.450 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.450 | |
| 2bal | PQA | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 2pau | D5M | 5'-deoxynucleotidase YfbR | / | 0.450 | |
| 3d2r | ADP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | 2.7.11.2 | 0.450 | |
| 3d7k | D7K | Benzaldehyde lyase | / | 0.450 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.450 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.450 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4n9w | GDP | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.450 | |
| 4ng2 | OHN | Transcriptional activator protein LasR | / | 0.450 | |
| 5dbv | COA | Aldehyde Dehydrogenase | / | 0.450 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.449 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.449 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.449 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 1uu9 | BI3 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.448 | |
| 2brb | PFQ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.448 | |
| 3iph | G11 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 5cnn | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.448 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.447 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.447 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.447 | |
| 3c1t | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.447 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.447 | |
| 3irm | 1CY | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.447 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.446 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.446 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.446 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.446 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.446 | |
| 3p3z | P3Z | Putative cytochrome P450 | / | 0.446 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.446 | |
| 5iw5 | NMN | NADH pyrophosphatase | / | 0.446 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.445 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.445 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.445 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.445 | |
| 1d2s | DHT | Sex hormone-binding globulin | / | 0.444 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.444 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.444 | |
| 1szm | BI4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.444 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.444 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.444 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.444 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.444 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.444 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.443 | |
| 1tys | TMP | Thymidylate synthase | / | 0.443 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.443 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.443 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 2zsi | GA4 | Gibberellin receptor GID1A | 3 | 0.443 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 4ach | KDI | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.443 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 4qq3 | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.443 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.442 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.442 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2bxm | IMN | Serum albumin | / | 0.442 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 3b9l | AZZ | Serum albumin | / | 0.442 | |
| 3ms4 | 21N | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.442 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.442 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.442 | |
| 4hai | I23 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.442 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 2brm | DFZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.441 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.441 | |
| 3d5q | T30 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.441 | |
| 4jql | VJ6 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4lk3 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.441 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.440 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.440 | |
| 3uqd | ADP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.440 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.440 | |
| 4ap1 | FAD | Steroid monooxygenase | / | 0.440 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.440 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.440 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.440 |