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 |
|---|---|---|---|
| 5kf2 | COA | Predicted acetyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 5kf2 | COA | Predicted acetyltransferase | / | 1.000 | |
| 5kf9 | COA | Predicted acetyltransferase | / | 0.634 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.589 | |
| 5kf1 | COA | Predicted acetyltransferase | / | 0.562 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.548 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.547 | |
| 2wpw | ACO | Orf14 | / | 0.546 | |
| 3f0a | ACO | Spermidine N(1)-acetyltransferase | / | 0.542 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.537 | |
| 2wpx | ACO | Orf14 | / | 0.534 | |
| 2cy2 | ACO | Probable acetyltransferase | / | 0.526 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.524 | |
| 4cs0 | ACO | PanD regulatory factor | / | 0.522 | |
| 4cry | ACO | PanD regulatory factor | / | 0.512 | |
| 5kf8 | COA | Predicted acetyltransferase | / | 0.509 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.508 | |
| 4crz | ACO | PanD regulatory factor | / | 0.508 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.508 | |
| 4ag9 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.503 | |
| 4mxe | ACO | N-acetyltransferase ESCO1 | 2.3.1 | 0.502 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.497 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.493 | |
| 4at4 | T6E | BDNF/NT-3 growth factors receptor | 2.7.10.1 | 0.493 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.492 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.487 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.487 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.487 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.485 | |
| 2b1z | 17M | Estrogen receptor | / | 0.483 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.482 | |
| 2vez | ACO | Glucosamine 6-phosphate acetyltransferase, putative | / | 0.479 | |
| 5kf2 | ACO | Predicted acetyltransferase | / | 0.477 | |
| 3pgp | ACO | Uncharacterized protein | / | 0.475 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.474 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 3p9t | TCL | Repressor | / | 0.473 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.473 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.472 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.470 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 2ewa | SB2 | Mitogen-activated protein kinase 14 | / | 0.469 | |
| 4equ | G6I | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.468 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.468 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.468 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.467 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2jdc | CAO | Probable acetyltransferase | / | 0.466 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.466 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.464 | |
| 4ybn | FAD | Flavin-nucleotide-binding protein | / | 0.464 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.464 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 3oll | EST | Estrogen receptor beta | / | 0.463 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.463 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.461 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.460 | |
| 5kf1 | ACO | Predicted acetyltransferase | / | 0.460 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3gya | COA | GCN5-related N-acetyltransferase | / | 0.459 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 4y1b | NAP | AntE | / | 0.459 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.459 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2rl5 | 2RL | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.458 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.458 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2pl0 | STI | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.457 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.457 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.456 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.456 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.455 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.455 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.454 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3kr6 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.454 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.454 | |
| 1xng | DND | NH(3)-dependent NAD(+) synthetase | 6.3.1.5 | 0.453 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.453 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4g1c | CNA | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.453 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.453 | |
| 4keb | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2jc6 | QPP | Calcium/calmodulin-dependent protein kinase type 1D | 2.7.11.17 | 0.451 | |
| 3eta | 351 | Insulin receptor | 2.7.10.1 | 0.451 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.451 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.451 | |
| 4fk3 | 325 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.451 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.451 | |
| 3exn | ACO | Probable acetyltransferase | / | 0.450 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.450 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.449 | |
| 3up3 | XCA | aceDAF-12 | / | 0.449 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 5kgj | ACO | Predicted acetyltransferase | / | 0.449 | |
| 1r2j | FAD | FkbI | / | 0.448 | |
| 2obx | INI | 6,7-dimethyl-8-ribityllumazine synthase 2 | 2.5.1.78 | 0.448 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2x7b | COA | N-alpha-acetyltransferase | 2.3.1 | 0.447 | |
| 2xkc | 4VQ | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.447 | |
| 3r1k | COA | N-acetyltransferase Eis | / | 0.447 | |
| 3sxn | COA | N-acetyltransferase Eis | / | 0.447 | |
| 4u7w | NDP | MxaA | / | 0.447 | |
| 4ua3 | COA | N-alpha-acetyltransferase 40 | 2.3.1 | 0.447 | |
| 1ib1 | COT | Serotonin N-acetyltransferase | / | 0.446 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.446 | |
| 3gy9 | COA | GCN5-related N-acetyltransferase | / | 0.446 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.446 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.446 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.446 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.446 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.446 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.445 | |
| 1xp9 | AIJ | Estrogen receptor | / | 0.445 | |
| 2p1d | SAH | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.444 | |
| 1olm | VTQ | SEC14-like protein 2 | / | 0.444 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.444 | |
| 3c3e | FO1 | 2-phospho-L-lactate transferase | / | 0.444 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.444 | |
| 3zsg | T75 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 4blc | NDP | Catalase | 1.11.1.6 | 0.444 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.443 | |
| 2vxk | COA | Glucosamine 6-phosphate acetyltransferase, putative | / | 0.443 | |
| 3lq2 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.443 | |
| 3nxr | D2D | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2fm0 | M98 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 3huc | G97 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 4eqs | COA | Coenzyme A disulfide reductase | / | 0.442 | |
| 4j6c | STR | Cytochrome P450 monooxygenase | / | 0.442 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.442 | |
| 1dgb | NDP | Catalase | 1.11.1.6 | 0.441 | |
| 1wpg | ADP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.441 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.441 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.441 | |
| 2pda | TPP | Pyruvate synthase | / | 0.441 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.441 | |
| 3s6f | COA | Uncharacterized protein | / | 0.441 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.441 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.441 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.441 | |
| 5c88 | COA | N-alpha-acetyltransferase | / | 0.441 | |
| 1dli | UDX | UDP-glucose 6-dehydrogenase | / | 0.440 | |
| 3dge | ADP | Sensor histidine kinase | / | 0.440 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3hu2 | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.440 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.440 |