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 |
|---|---|---|---|
| 4rr9 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4rr9 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 1.000 | |
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.648 | |
| 4rrh | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.629 | |
| 4rrb | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.627 | |
| 4rrm | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.627 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.622 | |
| 4rr8 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.622 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.608 | |
| 4rrc | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.607 | |
| 4rrd | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.602 | |
| 4rrl | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.592 | |
| 4rrj | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.575 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.558 | |
| 4rra | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.553 | |
| 4rrk | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.542 | |
| 3pd2 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.531 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.523 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.519 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.517 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.514 | |
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 0.510 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.500 | |
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.494 | |
| 3pd3 | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.488 | |
| 4rrf | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.485 | |
| 1nhz | 486 | Glucocorticoid receptor | / | 0.484 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.481 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.477 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.476 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.473 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3inr | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.471 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.470 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.470 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.469 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.467 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.467 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.467 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.466 | |
| 3pd5 | TSB | Threonine--tRNA ligase | 6.1.1.3 | 0.466 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.466 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.466 | |
| 4xwt | U5P | Ribonuclease J | / | 0.466 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 3pwh | ZMA | Adenosine receptor A2a | / | 0.465 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.464 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.463 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.463 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.459 | |
| 1ddt | APU | Diphtheria toxin | / | 0.458 | |
| 2e98 | B29 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.458 | |
| 4fw0 | 5KJ | Nitric oxide synthase, brain | 1.14.13.39 | 0.458 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.458 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 2vtd | LKM | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.456 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3ufp | H4W | Nitric oxide synthase, brain | 1.14.13.39 | 0.454 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.454 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1q23 | FUA | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.453 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.453 | |
| 3jx3 | JI5 | Nitric oxide synthase, brain | 1.14.13.39 | 0.453 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.453 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.453 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.452 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.452 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3up3 | XCA | aceDAF-12 | / | 0.452 | |
| 4b8z | GDP | GDP-L-fucose synthase | 1.1.1.271 | 0.452 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.452 | |
| 4kxj | P34 | Nucleoprotein | / | 0.452 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.451 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.451 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.450 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.450 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.450 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.450 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.449 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.449 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.449 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.448 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.448 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.448 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.447 | |
| 4nbi | D3Y | D-tyrosyl-tRNA(Tyr) deacylase | / | 0.447 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.446 | |
| 1m9j | CLW | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.446 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.446 | |
| 4lsj | LSJ | Glucocorticoid receptor | / | 0.446 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.446 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.445 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.445 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.445 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.445 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.444 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.444 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4jse | QJ2 | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.444 | |
| 1dtp | APU | Diphtheria toxin | / | 0.443 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.443 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.443 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.443 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.443 | |
| 1xp6 | AIU | Estrogen receptor | / | 0.442 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.442 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3af0 | GDP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.442 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.442 | |
| 4imt | 1EW | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 4lux | QJ8 | Nitric oxide synthase, brain | 1.14.13.39 | 0.442 | |
| 2fk8 | SAM | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.441 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.441 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.441 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.441 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.441 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.441 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.441 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.441 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.440 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.440 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.440 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 |