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 |
|---|---|---|---|
| 2ji5 | UTP | Uridylate kinase | 2.7.4.22 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ji5 | UTP | Uridylate kinase | 2.7.4.22 | 1.000 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.548 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.511 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.489 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.489 | |
| 2j4k | U5P | Uridylate kinase | 2.7.4.22 | 0.477 | |
| 3ieu | GDP | GTPase Era | / | 0.473 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.472 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.471 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.470 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.470 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.469 | |
| 1h74 | AGS | Homoserine kinase | 2.7.1.39 | 0.467 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.467 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.465 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.464 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.464 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.463 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.460 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.459 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.458 | |
| 1pjk | ANP | Casein kinase II subunit alpha | 2.7.11.1 | 0.458 | |
| 4i9b | NAD | Putative betaine aldehyde dehyrogenase | / | 0.458 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.457 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.456 | |
| 1tqp | ATP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.455 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.455 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.455 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 4jin | 1L7 | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.454 | |
| 2aa0 | MTP | Adenosine kinase | 2.7.1.20 | 0.453 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.453 | |
| 3lm9 | ADP | Putative fructokinase | 2.7.1.4 | 0.453 | |
| 3zhx | FM6 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.453 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.453 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.452 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.452 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.452 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.451 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.451 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.451 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.450 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.450 | |
| 1gqt | ACP | Ribokinase | / | 0.449 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.449 | |
| 2j4l | UTP | Uridylate kinase | 2.7.4.22 | 0.449 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.448 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.447 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.447 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.447 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 4nwi | CTN | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.447 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.446 | |
| 1tqm | ANP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.446 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.446 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.446 | |
| 4gav | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.446 | |
| 4hle | 17V | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 1dnp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.445 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2vf3 | GVS | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 3gxf | IFM | Glucosylceramidase | 3.2.1.45 | 0.445 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.445 | |
| 1eyq | NAR | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.444 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.444 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3cis | ATP | Universal stress protein Rv2623 | / | 0.444 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.444 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.444 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4u97 | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.444 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.443 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 3dj4 | UD1 | Bifunctional protein GlmU | / | 0.443 | |
| 3q7d | NPX | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.443 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.443 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.442 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.442 | |
| 3o15 | 3NM | Thiamine-phosphate synthase | / | 0.442 | |
| 3o15 | IFP | Thiamine-phosphate synthase | / | 0.442 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.442 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.442 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.442 | |
| 4jic | FMN | GTN Reductase | / | 0.442 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.442 | |
| 1cf2 | NAP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 1loo | GTP | Adenylosuccinate synthetase isozyme 1 | / | 0.441 | |
| 2eau | CZA | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.441 | |
| 2v1x | ADP | ATP-dependent DNA helicase Q1 | 3.6.4.12 | 0.441 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.441 | |
| 3rn8 | RN8 | Glutamate receptor 2 | / | 0.441 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 4zol | ACP | Tubulin tyrosine ligase | / | 0.441 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.440 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.440 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.440 |