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 |
|---|---|---|---|
| 3vpb | ADP | Glutamate--LysW ligase ArgX | 6.3.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3vpb | ADP | Glutamate--LysW ligase ArgX | 6.3.2 | 1.000 | |
| 3vpc | ADP | Glutamate--LysW ligase ArgX | 6.3.2 | 0.527 | |
| 3qc9 | ADP | Rhodopsin kinase | / | 0.508 | |
| 4ftr | 5HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.490 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.478 | |
| 4ftt | 6HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.476 | |
| 4kgm | ATP | Uncharacterized protein | / | 0.475 | |
| 1ny3 | ADP | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.474 | |
| 3wo0 | ADP | Alanine--anticapsin ligase | / | 0.472 | |
| 4l9i | 8PR | Rhodopsin kinase | / | 0.471 | |
| 2r7b | 253 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.468 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.467 | |
| 4ft0 | HK9 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.466 | |
| 3s87 | DGT | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.465 | |
| 4bfm | ANP | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.465 | |
| 1pk8 | ATP | Synapsin-1 | / | 0.464 | |
| 4rrv | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.464 | |
| 4fsw | HK6 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.461 | |
| 4hyh | 1AM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.461 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 4qny | ANP | Mitogen activated protein kinase, putative | / | 0.460 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.459 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.458 | |
| 2w4k | ADP | Death-associated protein kinase 1 | 2.7.11.1 | 0.457 | |
| 2wmu | ZYU | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.457 | |
| 3c4w | ATP | Rhodopsin kinase | / | 0.457 | |
| 3hrc | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.457 | |
| 3wo1 | ADP | Alanine--anticapsin ligase | / | 0.456 | |
| 1ol6 | ATP | Aurora kinase A | 2.7.11.1 | 0.455 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.455 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.455 | |
| 3r2b | 05B | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.455 | |
| 1j1c | ADP | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.454 | |
| 2acx | ANP | G protein-coupled receptor kinase 6 | 2.7.11.16 | 0.454 | |
| 3tki | S25 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.454 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.454 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.453 | |
| 2bro | DF2 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.453 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.452 | |
| 2pyw | ADP | Methylthioribose kinase | 2.7.1.100 | 0.452 | |
| 2r4t | ADP | Glycogen synthase | 2.4.1.21 | 0.452 | |
| 3hrf | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.451 | |
| 4fsn | A58 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.451 | |
| 3tw6 | ADP | Pyruvate carboxylase | / | 0.449 | |
| 2hog | 710 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.448 | |
| 4s33 | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.448 | |
| 4ohw | ATP | Protein clpf-1 | / | 0.447 | |
| 1sxj | AGS | Replication factor C subunit 1 | / | 0.446 | |
| 3qcy | 3Q3 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 3s8a | DGT | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.446 | |
| 4aw0 | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.446 | |
| 4ftu | 7HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 3t8o | ATP | Rhodopsin kinase | / | 0.445 | |
| 3wnz | ADP | Alanine--anticapsin ligase | / | 0.445 | |
| 4ft7 | H3K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.445 | |
| 4ji9 | 1M3 | Tyrosine-protein kinase JAK2 | / | 0.445 | |
| 4rqk | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.445 | |
| 1cs4 | GSP | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | / | 0.444 | |
| 2cgx | 3D3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.444 | |
| 4gv8 | DUP | DUTPase | / | 0.444 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.444 | |
| 1phk | ATP | Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform | 2.7.11.19 | 0.443 | |
| 2ayp | 43A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.443 | |
| 2ijm | ATP | Focal adhesion kinase 1 | 2.7.10.2 | 0.443 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.443 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 2xvv | 9DN | Serum albumin | / | 0.442 | |
| 3c4z | ADP | Rhodopsin kinase | / | 0.442 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.442 | |
| 4bl1 | ANP | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.442 | |
| 4o1p | ANP | Ribonuclease L | / | 0.442 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.442 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2w4j | ADP | Death-associated protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3sdi | 3SD | Proteasome subunit beta type-5 | 3.4.25.1 | 0.441 | |
| 3sdi | 3SD | Proteasome subunit beta type-6 | 3.4.25.1 | 0.441 | |
| 5c1o | ANP | D-alanine--D-alanine ligase | / | 0.441 | |
| 2biy | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 2v0u | FMN | NPH1-1 | / | 0.440 | |
| 3t99 | ADP | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | / | 0.440 | |
| 4lrj | ANP | Uncharacterized protein | / | 0.440 |