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 |
|---|---|---|---|
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 1.000 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.856 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.838 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.743 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.741 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.717 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.687 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.681 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.653 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.648 | |
| 1eny | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.631 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.615 | |
| 2ntv | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.606 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.592 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.590 | |
| 2idz | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.588 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.583 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.571 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.566 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.565 | |
| 5cpb | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.562 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.561 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.559 | |
| 1enz | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.545 | |
| 1p44 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.531 | |
| 4bgi | I4I | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.527 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.526 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.525 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.521 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.520 | |
| 2b36 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.506 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.502 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.499 | |
| 2b35 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.497 | |
| 3g5h | YTT | Mycocyclosin synthase | 1.14.21.9 | 0.493 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.493 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.487 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.480 | |
| 2y3s | TIR | TamL | / | 0.478 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.478 | |
| 2ntj | P1H | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.476 | |
| 2y3r | TRK | TamL | / | 0.476 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.476 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.475 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.474 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.472 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.472 | |
| 2y4g | TIR | TamL | / | 0.470 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.470 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.468 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.468 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.465 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.465 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.464 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.463 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.463 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.461 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.461 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.460 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.459 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.459 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.458 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.458 | |
| 4qec | NAP | ElxO | / | 0.457 | |
| 4qed | NAP | ElxO | / | 0.457 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.456 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.456 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.455 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.454 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.454 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.454 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.453 | |
| 1nyx | DRF | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.452 | |
| 1jg0 | DDT | Thymidylate synthase | / | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.451 | |
| 4ktl | 1CQ | Cytochrome P450 | / | 0.451 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.450 | |
| 4aw3 | MYV | Mycinamicin IV hydroxylase/epoxidase | / | 0.450 | |
| 1ee9 | NAD | Methylenetetrahydrofolate dehydrogenase [NAD(+)] | 1.5.1.15 | 0.449 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.449 | |
| 4ips | 1G4 | Mycocyclosin synthase | 1.14.21.9 | 0.449 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.449 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.448 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.448 | |
| 3sgv | 2BJ | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.448 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.448 | |
| 4g48 | PZB | Mycocyclosin synthase | 1.14.21.9 | 0.448 | |
| 4jnc | 1LF | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.448 | |
| 4kwh | NAP | Reductase homolog | / | 0.448 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.447 | |
| 1xds | DRA | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.447 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.447 | |
| 1t2b | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.446 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.446 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 3nxu | RIT | Cytochrome P450 3A4 | / | 0.446 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.446 | |
| 4l0q | NAD | Alcohol dehydrogenase class-3 | / | 0.446 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 1uyu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.445 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.445 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3tmz | 06X | Cytochrome P450 2B4 | 1.14.14.1 | 0.445 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.444 | |
| 1m9m | 6NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.444 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.444 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.444 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.444 | |
| 4nky | 3QZ | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 2gna | GDU | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.443 | |
| 2jcx | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.443 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.443 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.443 | |
| 3vt6 | 5YI | Vitamin D3 receptor | / | 0.443 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.443 | |
| 4ict | 1ED | Mycocyclosin synthase | 1.14.21.9 | 0.443 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.443 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.442 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.442 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.442 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.442 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.442 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.441 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.441 | |
| 1vzd | CB3 | Thymidylate synthase | / | 0.441 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.441 | |
| 2jfg | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.441 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.441 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.441 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.441 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.440 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.440 | |
| 3bmo | NAP | Pteridine reductase | / | 0.440 | |
| 3c0g | 3AM | Peripheral plasma membrane protein CASK | 2.7.11.1 | 0.440 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.440 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4o59 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.440 |