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 |
|---|---|---|---|
| 1z6l | FAD | Polyamine oxidase FMS1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 1.000 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.619 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.615 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.613 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.605 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.601 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.600 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.593 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.590 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.561 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.555 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.551 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.541 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.540 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.539 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.537 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.535 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.527 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.521 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.519 | |
| 3nn6 | HNK | 6-hydroxy-L-nicotine oxidase | / | 0.518 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.514 | |
| 3we0 | FAD | Lysine 2-monooxygenase | / | 0.499 | |
| 2uxx | FAJ | Lysine-specific histone demethylase 1A | 1 | 0.495 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.495 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.492 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.479 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.474 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.473 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.470 | |
| 1aj2 | 2PH | Dihydropteroate synthase | / | 0.466 | |
| 2pui | ADP | Methylthioribose kinase | 2.7.1.100 | 0.465 | |
| 2jae | FAD | L-amino acid oxidase | / | 0.464 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.464 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.462 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.461 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.461 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.460 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.459 | |
| 3x04 | GNP | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | 2.7.1.149 | 0.459 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.457 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.456 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.453 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.451 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.451 | |
| 3t3i | GPW | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.451 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.451 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.450 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.450 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.449 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.448 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.447 | |
| 3e8x | NAP | BH1520 protein | / | 0.447 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.447 | |
| 2bac | FAD | Putative aminooxidase | / | 0.446 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.446 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.446 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.446 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.446 | |
| 4l4x | NDP | AmphI | / | 0.446 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.445 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.444 | |
| 2owb | 626 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.443 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.443 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.442 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3v2u | ATP | Protein GAL3 | / | 0.442 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.441 | |
| 3up5 | NAP | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.441 | |
| 4brd | ANP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.441 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.440 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.440 | |
| 2dek | SAH | Diphthine synthase | / | 0.440 | |
| 2xvv | 9DN | Serum albumin | / | 0.440 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.440 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.440 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.440 |