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 |
|---|---|---|---|
| 3gya | COA | GCN5-related N-acetyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3gya | COA | GCN5-related N-acetyltransferase | / | 1.000 | |
| 3gy9 | COA | GCN5-related N-acetyltransferase | / | 0.769 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.587 | |
| 5kf2 | ACO | Predicted acetyltransferase | / | 0.583 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.574 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.571 | |
| 5kgj | ACO | Predicted acetyltransferase | / | 0.567 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.566 | |
| 1b87 | ACO | Aac(6')-Ii protein | / | 0.557 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.557 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.549 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.547 | |
| 3exn | ACO | Probable acetyltransferase | / | 0.546 | |
| 1j4j | ACO | Acetyltransferase | 2.3.1 | 0.540 | |
| 5kf1 | ACO | Predicted acetyltransferase | / | 0.536 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.525 | |
| 5kf1 | COA | Predicted acetyltransferase | / | 0.522 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.515 | |
| 2jdd | ACO | Probable acetyltransferase | / | 0.514 | |
| 2fxf | ACO | Diamine acetyltransferase 1 | / | 0.512 | |
| 4ag9 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.504 | |
| 4xnh | ACO | N-terminal acetyltransferase A complex subunit NAT5 | 2.3.1 | 0.503 | |
| 1cjw | COT | Serotonin N-acetyltransferase | / | 0.502 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.502 | |
| 1ib1 | COT | Serotonin N-acetyltransferase | / | 0.500 | |
| 1kux | CA3 | Serotonin N-acetyltransferase | / | 0.500 | |
| 2bei | ACO | Diamine acetyltransferase 2 | 2.3.1.57 | 0.500 | |
| 4zm6 | ACO | N-acetyl-beta-D glucosaminidase | / | 0.500 | |
| 2jdc | CAO | Probable acetyltransferase | / | 0.499 | |
| 1l0c | COT | Serotonin N-acetyltransferase | / | 0.498 | |
| 5kf9 | COA | Predicted acetyltransferase | / | 0.498 | |
| 2bsw | CAO | Probable acetyltransferase | / | 0.495 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.492 | |
| 4mxe | ACO | N-acetyltransferase ESCO1 | 2.3.1 | 0.492 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.492 | |
| 3bj7 | COA | Diamine acetyltransferase 1 | / | 0.490 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.488 | |
| 3u4r | 08F | Genome polyprotein | 2.7.7.48 | 0.488 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.485 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.484 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.483 | |
| 3f0a | ACO | Spermidine N(1)-acetyltransferase | / | 0.483 | |
| 2b3v | ACO | Diamine acetyltransferase 1 | / | 0.481 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.480 | |
| 3zj0 | ACO | Putative acetyltransferase OgpAT | / | 0.479 | |
| 1qsr | ACO | HAT A1 | / | 0.475 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.474 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.474 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.473 | |
| 1axw | MTX | Thymidylate synthase | / | 0.472 | |
| 2wpx | ACO | Orf14 | / | 0.472 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.472 | |
| 5kf2 | COA | Predicted acetyltransferase | / | 0.472 | |
| 2amb | 17H | Androgen receptor | / | 0.471 | |
| 2fiw | ACO | GCN5-related N-acetyltransferase:Aminotransferase, class-II | / | 0.471 | |
| 2wpw | ACO | Orf14 | / | 0.471 | |
| 5kf8 | COA | Predicted acetyltransferase | / | 0.471 | |
| 4crz | ACO | PanD regulatory factor | / | 0.470 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.469 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.468 | |
| 1kmv | LII | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.466 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.466 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2xvw | 9NR | Serum albumin | / | 0.463 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3s6f | COA | Uncharacterized protein | / | 0.461 | |
| 4cry | ACO | PanD regulatory factor | / | 0.461 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1jtq | LY3 | Thymidylate synthase | / | 0.460 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.460 | |
| 1s5k | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.460 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3uph | 0C1 | Genome polyprotein | 2.7.7.48 | 0.460 | |
| 4hyf | 1AK | Tankyrase-2 | 2.4.2.30 | 0.459 | |
| 3tyv | HI3 | Genome polyprotein | 2.7.7.48 | 0.458 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3ksl | SZH | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.457 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.457 | |
| 2cy2 | ACO | Probable acetyltransferase | / | 0.456 | |
| 3b9l | AZZ | Serum albumin | / | 0.456 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.456 | |
| 1dtp | APU | Diphtheria toxin | / | 0.455 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.455 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.455 | |
| 1syn | F89 | Thymidylate synthase | / | 0.454 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 4cs0 | ACO | PanD regulatory factor | / | 0.454 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.453 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.453 | |
| 3vg9 | ZMA | Adenosine receptor A2a | / | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1t7t | DHT | Androgen receptor | / | 0.452 | |
| 2pit | DHT | Androgen receptor | / | 0.452 | |
| 3mgd | ACO | Predicted acetyltransferase | / | 0.452 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.452 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.452 | |
| 5h84 | 1VU | Histone acetyltransferase KAT2A | 2.3.1.48 | 0.452 | |
| 1k27 | MTM | S-methyl-5'-thioadenosine phosphorylase | / | 0.451 | |
| 3pgp | ACO | Uncharacterized protein | / | 0.451 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.451 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.451 | |
| 1daj | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3ehj | ACP | Sensor histidine kinase DesK | 2.7.13.3 | 0.450 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.450 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4mka | 2AY | Genome polyprotein | 2.7.7.48 | 0.450 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.449 | |
| 1udt | VIA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.449 | |
| 3h2l | YAK | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 3ntz | 3TZ | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3rs0 | GNP | GTPase HRas | / | 0.449 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.449 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3qly | 55V | Uncharacterized protein | / | 0.448 | |
| 4hlm | 16S | Tankyrase-2 | 2.4.2.30 | 0.448 | |
| 1ie9 | VDX | Vitamin D3 receptor | / | 0.447 | |
| 1k0c | GTB | Transcriptional regulator URE2 | / | 0.447 | |
| 1tsd | F89 | Thymidylate synthase | / | 0.447 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.447 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.447 | |
| 2rgc | GNP | GTPase HRas | / | 0.447 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.447 | |
| 1al7 | HST | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.446 | |
| 1dna | CB3 | Thymidylate synthase | / | 0.446 | |
| 1hfp | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1lhu | EST | Sex hormone-binding globulin | / | 0.446 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.446 | |
| 1zpr | CB3 | Thymidylate synthase | / | 0.446 | |
| 2zb8 | IMN | Prostaglandin reductase 2 | 1.3.1.48 | 0.446 | |
| 3ghv | GHC | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1m4d | COA | Aminoglycoside 2'-N-acetyltransferase | 2.3.1 | 0.445 | |
| 1pua | COA | HAT A1 | / | 0.445 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 3vmm | P0D | Alanine--anticapsin ligase | / | 0.445 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.445 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.444 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2xvv | 9DN | Serum albumin | / | 0.444 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3br9 | DEY | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 3dr1 | C5D | Vitamin D3 receptor A | / | 0.444 | |
| 3nwl | NDP | Catalase | 1.11.1.6 | 0.444 | |
| 4ua3 | COA | N-alpha-acetyltransferase 40 | 2.3.1 | 0.444 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.444 | |
| 4ug2 | NGI | Adenosine receptor A2a | / | 0.444 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.443 | |
| 2aax | PDN | Mineralocorticoid receptor | / | 0.443 | |
| 2ama | DHT | Androgen receptor | / | 0.443 | |
| 2b00 | GCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.443 | |
| 2jj2 | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 2onf | COA | Uncharacterized protein | / | 0.443 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1nce | CB3 | Thymidylate synthase | / | 0.442 | |
| 1rdt | L79 | Retinoic acid receptor RXR-alpha | / | 0.442 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.442 | |
| 1t7r | DHT | Androgen receptor | / | 0.442 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.442 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.442 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.442 | |
| 2vcz | VC3 | Hematopoietic prostaglandin D synthase | / | 0.442 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.442 | |
| 3bqd | DAY | Glucocorticoid receptor | / | 0.442 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.442 | |
| 3ew2 | BTN | Hypothetical conserved protein | / | 0.442 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.442 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.442 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1lke | DOG | Bilin-binding protein | / | 0.441 | |
| 2azy | CHD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.441 | |
| 2zpa | ACO | tRNA(Met) cytidine acetyltransferase TmcA | / | 0.441 | |
| 4edz | 0O5 | Hematopoietic prostaglandin D synthase | / | 0.441 | |
| 4f5d | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 4jhi | EMU | Nodulin-13 | / | 0.441 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.441 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.440 | |
| 2gzl | 2AA | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.440 |